784 tool(s) found

Tool Description Topics Available version(s)
A) Format Data for LEfSe 2
aaChanges amino-acid changes caused by a set of SNPs 2
Add BLAST links to a mothur OTU table 1
Add column to an existing dataset 3
add-read-counts Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file 3
Add/Remove chr prefix add or remove chr prefix from a column 1
AddCommentsToBam add comments to BAM dataset 12
AddOrReplaceReadGroups add or replaces read group information 12
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
Align sequences using a variety of alignment methods (align_seqs) 2
Align.check Calculate the number of potentially misaligned bases 6
Align.seqs Align sequences to a template alignment 6
Amova Analysis of molecular variance 6
Analyze Covariates - draw plots 1
Analyze Seqz File using general R sequenza pipeline 1
Analyze statistical significance of sample groupings using distance matrices (compare_categories) 2
Annotate a VCF dataset with custom filters 1
Annotate Annotate VCF files using Ensemble VEP 1
Annotate with DGI database info 1
Annotate with DGI database info 1
AnnotateBed annotate coverage of features from multiple files 17
ANNOVAR Annotate a file using ANNOVAR 4
ANNOVAR Annotate a file using ANNOVAR 1
ANNOVAR Annotate VCF with functional information using ANNOVAR 2
Anosim Non-parametric multivariate analysis of changes in community structure 6
Apply Variant Recalibration 1
Apply Variant Recalibration 3
Assign taxonomy to each sequence (assign_taxonomy) 2
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
B) LDA Effect Size (LEfSe) 2
BAM to BED converter 19
BAM to fastq Convert BAM file to fastq 1
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 7
BAM-to-SAM convert BAM to SAM 7
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 7
Bandage Image visualize de novo assembly graphs 4
Bandage Info determine statistics of de novo assembly graphs 4
Bar chart for multiple columns 1
Base Recalibrator calculates covariates used to recalibrate base quality scores of reads 3
Baseline Bayesian Estimation of Antigen-Driven Selection 1
Baseline generator Generate baseline fasta file 1
bcftools view Converts BCF format to VCF format 11
BEAM significant single- and multi-locus SNP associations in case-control studies 1
BED to BAM converter 17
BED to IGV create batch script for taking IGV screenshots 10
BED-to-bigBed converter Conversion 2
BED-to-GFF converter 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 16
BEDPE to BAM converter 17
BedToIntervalList convert coordinate data into picard interval list format 12
Bin.seqs Order Sequences by OTU 6
Biom.info create shared and taxonomy files from biom 3
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
Bowtie2 - map reads against reference genome 21
Boxplot of quality statistics 2
BreakDancerMax 1
Build a UPGMA tree comparing samples (upgma_cluster) 2
C) Plot LEfSe Results 2
Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity) 2
Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables (beta_diversity) 2
Call and phase heterozygous SNPs 5
CallDiff Compares two Complete Genomics variant files. 2
Categorize by collapsing hierarchical data to a specified functional level 3
CG Normal Plot Create a CompleteGenomics-style normal Circos plot 1
CG Somatic Plot Create a CompleteGenomics-style somatic Circos plot 1
CG Tumor Plot Create a CompleteGenomics-style Tumor Circos plot 1
Change Case of selected columns 1
Check user's metadata mapping file for required data, valid format (validate_mapping_file) 2
Chimera.bellerophon Find putative chimeras using bellerophon 6
Chimera.ccode Find putative chimeras using ccode 6
Chimera.check Find putative chimeras using chimeraCheck 6
Chimera.perseus Find putative chimeras using chimeraCheck 6
Chimera.pintail Find putative chimeras using pintail 6
Chimera.slayer Find putative chimeras using slayer 6
Chimera.uchime Find putative chimeras using uchime 6
Chimera.vsearch find potential chimeric sequences using vsearch 3
Chop.seqs Trim sequences to a specified length 6
Circos Builder creates circos plots from standard bioinformatics datatypes. 3
Classify.otu Assign sequences to taxonomy 6
Classify.rf description 2
Classify.seqs Assign sequences to taxonomy 6
Classify.tree Get a consensus taxonomy for each node on a tree 6
CleanSam perform SAM/BAM grooming 12
Clearcut Generate a tree using relaxed neighbor joining 6
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 7
Closed-reference OTU picking Shotgun UniFrac workflow (pick_closed_reference_otus) 2
ClosestBed find the closest, potentially non-overlapping interval 17
Cluster Assign sequences to OTUs (Operational Taxonomic Unit) 6
Cluster.classic Assign sequences to OTUs (Dotur implementation) 6
Cluster.fragments Group sequences that are part of a larger sequence 6
Cluster.split Assign sequences to OTUs and split large matrices 5
ClusterBed cluster overlapping/nearby intervals 16
CML to InChI 2
CML to mol2 2
CML to SDF 2
cnv2igv VarDict is a variant discovery program. It can run in single sample, paired sample, or amplicon bias aware modes. 1
Collapse Collection into single dataset in order of the collection 5
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 12
Collect.shared Generate collector's curves for calculators on OTUs 6
Collect.single Generate collector's curves for OTUs 7
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 12
CollectGcBiasMetrics charts the GC bias metrics 12
CollectInsertSizeMetrics plots distribution of insert sizes 12
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 14
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 12
Column Regex Find And Replace 3
Column Select extract/rearrange columns from a tab-delimited file 1
Combine Variants 1
Combine Variants 3
Compare multiple VCF datasets 1
Compare BIOM tables Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples. 2
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 17
Compute an expression on every row 4
Compute beta diversity distance matrices and generate PCoA plots (beta_diversity_through_plots) 2
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 17
Concatenate datasets tail-to-head (cat) 7
Concatenate datasets tail-to-head 1
Condel Run Condel on SIFT, PolyPhen2 and MutationAssessor scores 1
Consensus.seqs Find a consensus sequence for each OTU or phylotype 6
Convert delimiters to TAB 1
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to fai file 1
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert from BAM to FastQ 13
Convert genome coordinates between assemblies and genomes 2
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 2
Convert lped to fped 2
Convert lped to plink pbed 2
Convert MAF to Fasta 2
Convert MAF to Genomic Intervals 2
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 2
Convert SAM to BAM 1
Convert tabular to dbnsfp 2
Convert, Merge, Randomize BAM datasets and perform other transformations 5
Cooccurrence tests whether presence-absence patterns differ from chance 6
Corr.axes correlation of data to axes 6
Correct counts in a mothur shared file for replicates and negative controls 1
Count occurrences of each record 2
Count Covariates on BAM files 1
Count.groups counts the number of sequences represented by a specific group or set of groups 6
Count.seqs (aka make.table) counts the number of sequences represented by the representative 6
Counttable totals add line with total counts to your mothur count table 1
Create assemblies with Unicycler Genome assembly 8
Create Germlines Change-O 1
Create Seqz File extracts the common positions containing A and B allele frequencies 1
Create single interval as a new dataset 1
Create text file with recurring lines 8
Create three-dimensional PCoA plots to be visualized with Emperor (make_emperor) 2
Create.database creates a database file from a list, repnames, repfasta and contaxonomy file 5
crr-2-fasta Convert fasta sequences into a single reference crr file 2
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 9
Cuffdata cummeRbund DB Create CummeRbund database 1
Cuffdata datasets history datasets from Cuffdiff output 1
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 10
Cuffdiff for cummeRbund find significant changes in transcript expression, splicing, and promoter use 1
Cuffdiff MDS Plot MultiDimensional Scaling (MDS) plot from cuffdiff read_group_tracking 1
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
Cuffnorm Create normalized expression levels 4
Cuffquant Precompute gene expression levels 4
cummeRbund R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output 1
Cut columns from a table (cut) 8
Cut columns from a table 2
Cutadapt Remove adapter sequences from Fastq/Fasta 16
D) Plot Cladogram 2
Data Fetch 1
DAVID functional annotation for a list of genes 1
DecodeCRR retreives the sequence for a given range of a chromosome. 2
Define Clones Change-O 1
Degap.seqs Remove gap characters from sequences 6
Deletion Profile calculates the distributions of deleted nucleotides across reads 3
Demultiplex 1
Demultiplex 1
Depth of Coverage on BAM files 3
Depth of Coverage on BAM files 1
DESeq2 Determines differentially expressed features from count tables Differential gene expression analysis 18
Deunique.seqs Return all sequences 6
Deunique.tree Reinsert the redundant sequence identiers back into a unique tree. 6
DEXSeq Determines differential exon usage from count tables 7
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 7
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 6
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 6
DotKnot pseudoknot prediction in a given RNA sequence 1
Downsample SAM/BAM Downsample a file to retain a subset of the reads 12
Dr. Disco (bam-extract) Extracts reads from two targeted regions 2
Dr. Disco (classify) Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists 2
Dr. Disco (detect) Detects break-points in RNA-seq 2
Dr. Disco (fix) Fixes chimeric alignments from STAR 2
Dr. Disco (integrate) Merges corresponding genomic breaks and exon-to-exon junctions 2
Draw ROC plot on "Perform LDA" output 2
Draw Stacked Bar Plots for different categories and different criteria 1
E) Plot One Feature 2
edgeR: Concatenate Expression Matrices Create a full expression matrix by selecting the desired columns from specific count tables 1
edgeR: Convert 'differentially expressed genes'-table to bedgraph(s) EdgeR's "differentially expressed genes" table to bedgraph(s) 2
edgeR: Design- from Expression matrix Create design- from an expression matrix 1
edgeR: Differential Gene(Expression) Analysis RNA-Seq gene expression analysis using edgeR (R package) 1
EGA Download streamer data from the European Genome-phenome Archive in a secure manner 2
ensemble_vcf integrates VCF files from different SNV detection methods for ensemble calling. 1
estimate-energy Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place 3
EstimateLibraryComplexity assess sequence library complexity from read sequences 12
Eval Variants 3
Eval Variants 1
ExpandBed replicate lines based on lists of values in columns 16
Extract Duplicates to a new dataset 1
Extract Element from a collection based on name 1
Extract element identifiers of a list collection 2
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 8
Extract MAF blocks given a set of genomic intervals 1
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract nanopore events from a set of sequencing reads 2
Extract Pairwise MAF blocks given a set of genomic intervals 1
extract-boxed-sequences Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility 3
F) Plot Differential Features 2
fasta-2-crr Convert fasta sequences into a single reference crr file 2
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 6
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 5
FASTQ to FASTA converter Conversion 6
FastQ Validator for each sequence in a file 1
fastq-join - Joins two paired-end reads on the overlapping ends 4
Fastq.info Convert fastq to fasta and quality 6
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 19
FastqToSam convert Fastq data into unaligned BAM 15
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 18
File Concatenation concatenate 2 files 1
Filter data on any column using simple expressions Formatting 1
Filter by quality Filtering 5
Filter Columns filter file based on column values 1
Filter fasta to remove sequences based on input criteria (filter_fasta) 2
Filter GFF data by attribute using simple expressions 3
Filter GFF data by feature count using simple expressions 2
Filter GTF data by attribute values_list 1
Filter MAF by specified attributes 1
Filter MAF blocks by Species 1
Filter MAF blocks by Size 1
Filter OTUs from an OTU table based on their observation counts or identifier (filter_otus_from_otu_table) 2
Filter sequence alignment by removing highly variable regions (filter_alignment) 2
Filter taxa from an OTU table (filter_taxa_from_otu_table) 2
Filter with SortMeRNA Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data 1
filter-annotated-entries Split entries into two files based on whether they overlap annotations in a bed file 3
filter-by-energy Split entries over two files based on the estimated energy 3
Filter.seqs removes columns from alignments 6
Filter.shared remove OTUs based on various critieria 6
Filters samples from an OTU table on the basis of the number of observations in that sample, or on the basis of sample metadata (filter_samples_from_otu_table) 2
FilterSamReads include or exclude aligned and unaligned reads and read lists 12
filtlong Filtering long reads by quality 1
FIMO - Find Individual Motif Occurrences 11
find-boxes Finds all occurances of two given boxes (sequence motifs) within a FASTA file 3
FisherBed calculate Fisher statistic between two feature files 16
fix-fasta-headers Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file 3
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 12
FlaiMapper detects small ncRNA derived fragments in small RNA-Seq data 4
FlankBed create new intervals from the flanks of existing intervals 17
Flye assembly of long and error-prone reads 3
Format tree and trait tables 2
FPKM Count calculates raw read count, FPM, and FPKM for each gene 5
FuMa match detected fusion genes based on gene names (in particular for RNA-Seq) 2
g:Profiler tools for functional profiling of gene lists 1
GBK-to-GFF converter 2
GEMINI actionable_mutations Retrieve genes with actionable somatic mutations via COSMIC and DGIdb 3
GEMINI amend Amend an already loaded GEMINI database. 4
GEMINI annotate the variants in an existing GEMINI database with additional information 6
GEMINI autosomal recessive/dominant Find variants meeting an autosomal recessive/dominant model 3
GEMINI burden perform sample-wise gene-level burden calculations 3
GEMINI comp_hets Identifying potential compound heterozygotes 3
GEMINI database info Retrieve information about tables, columns and annotation data stored in a GEMINI database 4
GEMINI de_novo Identifying potential de novo mutations 3
GEMINI dump Extract data from the Gemini DB 3
GEMINI fusions Identify somatic fusion genes from a GEMINI database 5
GEMINI gene_wise Discover per-gene variant patterns across families 3
GEMINI interactions Find genes among variants that are interacting partners 5
GEMINI load Loading a VCF file into GEMINI 7
GEMINI lof_sieve Filter LoF variants by transcript position and type 3
GEMINI mendel_errors Identify candidate violations of Mendelian inheritance 3
GEMINI pathways Map genes and variants to KEGG pathways 5
GEMINI qc Quality control tool 4
GEMINI query Querying the GEMINI database 4
GEMINI region Extracting variants from specific regions or genes 3
GEMINI roh Identifying runs of homozygosity 4
GEMINI set_somatic Tag somatic mutations in a GEMINI database 4
GEMINI stats Compute useful variant statistics 3
GEMINI windower Compute sliding window statistics from variants 4
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 9
Gene Body Coverage (Bigwig) Read coverage over gene body 9
Gene Cloud Plot creates a cloud plot where gene names are sized by mutation rate 1
Gene length and GC content from GTF and FASTA file 2
Generate A Matrix for using PC and LDA 1
Generic Genomic Data Plotter Generate scatterplot from genomic data 2
Genome Coverage compute the coverage over an entire genome 17
Get Microbial Data 1
Get VEP Cache Download and Index Genomes and Reference files used by Ensemble VEP 1
Get.communitytype description 6
Get.coremicrobiome fraction of OTUs for samples or abundances 6
Get.dists selects distances from a phylip or column file 6
Get.group group names from shared or from list and group 6
Get.groups Select groups 6
Get.label label names from list, sabund, or rabund file 6
Get.lineage Picks by taxon 6
Get.mimarkspackage creates a mimarks package form with your groups 6
Get.otulabels Selects OTU labels 6
Get.otulist Get otus for each distance in a otu list 6
Get.oturep Generate a fasta with a representative sequence for each OTU 6
Get.otus Get otus containing sequences from specified groups 6
Get.rabund Get rabund from a otu list or sabund 6
Get.relabund Calculate the relative abundance of each otu 6
Get.sabund Get sabund from a otu list or rabund 6
Get.seqs Picks sequences by name 6
Get.sharedseqs Get shared sequences at each distance from list and group 6
GetFastaBed use intervals to extract sequences from a FASTA file 16
GFA to FASTA Convert Graphical Fragment Assembly files to FASTA format 3
GFF-to-BED converter 1
GFF-to-BED converter Conversion 1
GFF-to-GTF converter 1
gffread Filters and/or converts GFF3/GTF2 records 6
GISTIC2.0 The GISTIC module identifies regions of the genome that are significantly amplified or deleted across a set of samples. 1
GPASS significant single-SNP associations in case-control studies 1
Group data by a column and perform aggregate operation on other columns. 5
GroupByBed group by common cols and summarize other cols 16
GTF-to-BEDGraph converter Conversion 1
GTF-to-GFF converter 1
Haplotype Caller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region 2
Hcluster Assign sequences to OTUs (Operational Taxonomic Unit) 2
Heatmap.bin Generate a heatmap for OTUs 6
Heatmap.sim Generate a heatmap for pariwise similarity 6
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 3
HISAT2 A fast and sensitive alignment program 17
Histogram of a numeric column 2
Histogram w ggplot2 4
HLA-DQ typing Determine possible associated types given BLAST IMGT/HLA annotation 1
Homova Homogeneity of molecular variance 6
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
iFUSE iFUSE: determine fusion gene candidates 1
iFUSE calc stats iFUSE description 1
IGV2Gistic Converts an IGV formatted segment file into an GISTIC2.0 compatible segment file. Requires exon BED file. Also produces an accompanying marker file in order to run GISTIC2.0. 1
IMGT Concatenate 1
IMGT Loader 1
IMGT Locus Split 1
Immune Repertoire pipeline 1
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
Indel Realigner - perform local realignment 3
Indel Realigner - perform local realignment 1
Indicator Identify indicator "species" for nodes on a tree 6
Infer Experiment speculates how RNA-seq were configured 9
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 9
Insertion Profile calculates the distribution of inserted nucleotides across reads 3
Integrative Plot Create a Circos plot with Complete Genomics and/or SNParray data 1
Intersect multiple VCF datasets 2
Intersect intervals find overlapping intervals in various ways 17
iReport create an HTML report 3
JaccardBed calculate the distribution of relative distances between two files 16
JBrowse genome browser 23
JBrowse - Data Directory to Standalone upgrades the bare data directory to a full JBrowse instance 22
Je-Demultiplex demultiplexes fastq files 2
Join Join two tsv files based on equal fields or overlapping regions. 2
Join the intervals of two datasets side-by-side Aggregation 5
Join two files 10
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
Junction Annotation compares detected splice junctions to reference gene model 9
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 9
JunctionDiff Reports difference between junction calls 2
Junctions Plot Create a Circos plot with Complete Genomics and/or SNParray data 1
Junctions2Events Groups related junctions and annotates each group with information about the structural rearrangement (event) that these junctions represent 2
Krona for mothur datasets 1
Krona pie chart from taxonomic profile 9
LAJ Pairwise Alignment Viewer 1
LAV to BED Converts a LAV formatted file to BED format 1
LD linkage disequilibrium and tag SNPs 1
Lefse description 6
Libshuff Cramer-von Mises tests communities for the same structure 6
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 16
List.otulabels Lists otu labels from shared or relabund file 6
List.seqs Lists the names (accnos) of the sequences 6
ListVariants Lists all variants present in CG var or masterVar file 2
Lollipop Plot gene summary plots 1
LPS LASSO-Patternsearch algorithm 1
LUMPY a probabilistic framework for structural variant discovery 2
MAF Coverage Stats Alignment coverage information 1
MAF Oncoplot summarizes top mutated genes by mutual exclusivity 1
MAF Summary Plot summarizes maf statistics into single multiplot 1
MAF to BED Converts a MAF formatted file to the BED format 1
MAF to FASTA Converts a MAF formatted file to FASTA format 1
MAF to Interval Converts a MAF formatted file to the Interval format 1
maf2maf Reannotates MAF file creating a new MAF file 1
maf2tdm Create a tdm file from a maf that was made using vcf2maf 1
Make Design Assign groups to Sets 6
Make multisample OTUtable from a shared and taxonomy file 1
Make phylogeny (make_phylogeny) 2
Make taxonomy summary charts based on taxonomy assignment (plot_taxa_summary) 2
Make VCF Converts masterVar and/or junction files to VCF. 2
Make.biom Make biom files from a shared file 6
Make.contigs Aligns paired forward and reverse fastq files to contigs as fasta and quality 6
Make.fastq Convert fasta and quality to fastq 6
Make.group Make a group file 6
Make.lefse create a lefse formatted input file from mothur's output files 6
Make.lookup allows you to create custom lookup files for use with shhh.flows 6
Make.shared Make a shared file from a list and a group 7
Make.sra creates the necessary files for a NCBI submission 6
MakeDB Change-O 1
MakeWindowsBed make interval windows across a genome 17
Manta SV Caller 1
Mantel Mantel correlation coefficient between two matrices. 6
Map with BWA - map short reads (< 100 bp) against reference genome 11
Map with BWA for Illumina 4
Map with BWA for SOLiD 2
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 12
Map with minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences 9
MapBed apply a function to a column for each overlapping interval 17
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 13
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 12
MaskFastaBed use intervals to mask sequences from a FASTA file 16
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
MeanQualityByCycle chart distribution of base qualities 12
MEME - Multiple Em for Motif Elicitation 10
Merge multiple VCF datasets 2
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 16
Merge Collections Merge a Collection of Files 1
Merge Columns together 2
Merge MAF Collection Merge a collection of MAF files 1
Merge paired reads Merges two fastq paired-reads files into one file. 1
Merge SEG Collection Merge a collection of SEG files 1
Merge.count Merge count tables 3
Merge.files Merge data 6
Merge.groups Merge groups in a shared file 6
Merge.sfffiles Merge SFF files 6
Merge.taxsummary Merge tax.summary files 6
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 12
MergeBED combine overlapping/nearby intervals into a single interval 16
MergeSamFiles merges multiple SAM/BAM datasets into one 12
Metagenome Contributions of OTUs to user-specified functions 2
MetaPhlAn2 to profile the composition of microbial communities 2
Metastats generate principle components plot data 6
Mimarks.attributes Reads bioSample Attributes xml and generates source for get.mimarkspackage command 6
miniasm Ultrafast de novo assembly for long noisy reads 4
Mismatch Profile calculates the distribution of mismatches across reads 3
MOL to CML 2
MOL to MOL2 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
Mothur OTUtable addBLAST for EMC workflow 2
Mothur OTUtable reformat for EMC workflow 1
Mothur summary of summaries useful for workflows 1
MOTHUR-combine-OTUtables concatenates 2 files admin 1
MOTHUR-prepare-multisample concatenates 2 files admin 1
Multi-Join (combine multiple files) 8
MultiCovBed counts coverage from multiple BAMs at specific intervals 16
Multiple Genome Analysis Combined 1
Multiple Genome Extract 1
Multiple Intersect identifies common intervals among multiple interval files 19
Mutation Analysis 1
MutationSeq a feature based classifier for somatic mutation detection 1
MutSpec Annot Annotate variants with ANNOVAR and other databases 2
MutSpec Compare Compare signatures with the cosine similarity method 2
MutSpec Filter Filter out variants present in public databases 2
MutSpec NMF Extract mutation signatures with the Non negative Matrix Factorization algorithm 2
MutSpec Split Split a tabular file by sample ID 2
MutSpec Stat Calculate various statistics on mutations 2
NanoPlot Plotting suite for Oxford Nanopore sequencing data and alignments 5
Nanopolish eventalign - Align nanopore events to reference k-mers 3
Nanopolish methylation - Classify nucleotides as methylated or not. 3
Nanopolish variants - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences 3
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 16
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 13
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 16
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 14
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 17
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 11
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 13
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
Newick Display Display a phylogenetic tree as SVG Phylogenetic tree visualisation 3
Newick Display visualize a phylogenetic tree Phylogenetic tree visualisation 2
Nmds generate non-metric multidimensional scaling data 6
Normalize the relative abundance of each OTU by the predicted number of 16S copies 3
Normalize a dataset by row or column sum to obtain proportion or percentage 1
Normalize.shared Normalize the number of sequences per group to a specified level 6
NormalizeFasta normalize fasta datasets 12
NucBed profile the nucleotide content of intervals in a FASTA file 17
Oncocircos creates a genome-centric visualization of SNV and CNV Data 1
OncodriveClust Run Oncodriveclust on mutations in cohort-wide MAF 1
OncodriveFM an approach to uncover driver genes or gene modules 1
OncoPrintPlus creates a summary matrix plot of cohort wide mutations 1
OncoSNPSeq characterising copy number alterations and loss-of-heterozygosity events in cancer samples from whole genome sequencing data 1
Oncostrip Plot Cohort-wide mutation oncostrip from MAF and (optionally) GISTIC data 1
Otu.association Calculate the correlation coefficient for the otus 6
Otu.hierarchy Relate OTUs at different distances 6
OverlapBed computes the amount of overlap from two intervals 16
Pairwise.seqs calculate uncorrected pairwise distances between sequences 6
Parse.list Generate a List file for each group 6
ParseDB Change-O 1
Parsimony Describes whether two or more communities have the same structure 6
PASS significant transcription factor binding sites from ChIP data 1
Paste two files side by side 1
Pca Principal Coordinate Analysis for a shared file 6
Pcoa Principal Coordinate Analysis for a distance matrix 5
Pcr.seqs Trim sequences 6
Pear Paired-End read merger 4
Perform alpha rarefaction (alpha_rarefaction) 2
Perform jackknifed UPGMA clustering and building jackknifed PCoA plots (jackknifed_beta_diversity) 2
Perform LDA Linear Discriminant Analysis 1
Perform open-reference OTU picking (pick_open_reference_otus) 2
Perform OTU picking (pick_otus) 2
Perform taxonomy summaries and plots (summarize_taxa_through_plots) 2
Phenotype Gene Relations 1
Phenotype Gene Relations plotting 1
Phylo.diversity Alpha Diversity calculates unique branch length 6
phyloP interspecies conservation scores 1
Phylotype Assign sequences to OTUs based on taxonomy 6
Pick representative set of sequences (pick_rep_set) 2
Pileup to VCF Converts a pileup to VCF with filtering 2
Pileup-to-Interval condenses pileup format into ranges of bases 4
pilon An automated genome assembly improvement and variant detection tool 2
Pindel Indel detection 3
PlasFlow Prediction of plasmid sequences in metagenomic contigs 1
Plot barplot with R 1
Plot heatmap of OTU table (make_otu_heatmap) 2
Plotting tool for multiple series and graph types 3
Plotting tool for multiple series and graph types and multiple output types 1
Porechop adapter trimmer for Oxford Nanopore reads 1
Pre.cluster Remove sequences due to pyrosequencing errors 6
Predict Metagenome based on the abundance of OTUs and a functional database 3
Primer.design identify sequence fragments that are specific to particular OTUs 6
Print Reads from BAM files 2
Print Reads on BAM files 3
PRISCA PRecISe Clonal Analysis 1
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 8
QC report from count tables 1
QDNAseq-export Export QDNAseq data to tabular 1
QDNAseq-regioning Perform regioning on QDNAseq data 1
QualityScoreDistribution chart quality score distribution 12
quick testing tool concatenates 2 files admin 1
R skeleton tool TEST TOOl 1
Racon Consensus module for raw de novo DNA assembly of long uncorrected reads. 2
RADIA identifies DNA variants in tumour/normal pairs 1
Rainfall Plot sample snv location summary plot 1
RandomBed generate random intervals in a genome 17
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 6
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 6
Read Distribution calculates how mapped reads were distributed over genome feature 9
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 7
Read GC determines GC% and read count 7
Read NVC to check the nucleotide composition bias 7
Read Quality determines Phred quality score 7
Realigner Target Creator for use in local realignment 3
Realigner Target Creator for use in local realignment 1
Recover samples discarded by sub.sample 1
Reduce Reads in BAM files 3
Regex Find And Replace 2
ReldistBed calculate the distribution of relative distances 16
Remove beginning of a file 1
Remove.dists Removes distances from a phylip or column file 6
Remove.groups Remove groups from groups,fasta,names,list,taxonomy 6
Remove.lineage Picks by taxon 6
Remove.otulabels Removes OTU labels 5
Remove.otus Removes OTUs from various file formats 6
Remove.rare Remove rare OTUs 6
Remove.seqs Remove sequences by name 6
Rename.seqs Rename sequences by concatenating the group name 3
ReorderSam reorder reads to match ordering in reference sequences 15
Replace parts of text 9
Replace Text in entire line 8
Replace Text in a specific column 8
ReplaceSamHeader replace header in a SAM/BAM dataset 15
reverse complement of DNA/RNA sequences 1
Reverse Complement a MAF file 1
Reverse.seqs Reverse complement the sequences 6
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 12
RevertSam revert SAM/BAM datasets to a previous state 12
RmDup remove PCR duplicates 7
RNA fragment size calculates the fragment size for each gene/transcript 5
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly 13
Roary the pangenome pipeline - Quickly generate a core gene alignment from gff3 files 5
RPKM Count calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 4
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 9
Run a core set of QIIME diversity analyses (core_diversity_analyses) 2
Run join_paired_ends on multiple files (multiple_join_paired_ends) 2
Run split_libraries_fastq on multiple files (multiple_split_libraries_fastq) 2
SAM-to-BAM convert SAM to BAM 11
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 17
Samtools fastx extract FASTA or FASTQ from alignment files 2
Samtools flagstat tabulate descriptive stats for BAM datset 8
samtools mpileup multi-way pileup of variants 9
Samtools parallel mpileup Samtools mpileup (supporting parallelization) 2
Screen.seqs Screen sequences 6
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
Search in textfiles (grep) 7
Secure Hash / Message Digest on a dataset 2
segmentation-fold RNA-Folding including predefined segments including K-turns 5
Select lines that match an expression 1
Select first lines from a dataset 1
Select first lines from a dataset (head) 8
Select last lines from a dataset 1
Select last lines from a dataset (tail) 8
Select Optimal Cluster Select the Optimal Clusters from TITAN 1
Select random lines from a file 2
Select Variants from VCF files 2
Select Variants from VCF files 3
Send file to owncloud send dataset to your Owncloud account on this server 1
Sens.spec Determine the quality of OTU assignment 6
Seq.error assess error rates in sequencing data 6
Sequenza Analysis and visualization of tumour sequencing data 1
SFF converter 1
Sffinfo Summarize the quality of sequences 6
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 6
Shhh.seqs Denoise program (Quince SeqNoise) 6
SHM & CSR pipeline 1
ShuffleBed randomly redistrubute intervals in a genome 17
Sickle windowed adaptive trimming of FASTQ data 5
SIFT predictions of functional sites 1
Simple Table Plotter 1
Simulate Illumina runs 1
Slice BAM by genomic regions 5
Slice VCF to get data from selected regions 1
SlopBed adjust the size of intervals 18
SNPDiff compares snp calls to a Complete Genomics variant file. 2
SnpEff databases: list available databases 12
SnpEff download: download a pre-built database 12
SnpEff eff: annotate variants 14
SomaticSniper calls SNVs for tumour-normal pairs. 1
Sort data in ascending or descending order 7
Sort data in ascending or descending order 2
Sort a row according to their columns 8
Sort Chromosomal Position sort file by chromosome, then by position 1
Sort.seqs put sequences in different files in the same order 6
SortBED order the intervals 16
SortSam sort SAM/BAM dataset 12
SpacingBed reports the distances between features 12
Split Dataset Pairs into two regular datasets 1
Split fastq libraries to performs demultiplexing of Fastq sequence data (split_libraries_fastq) 2
Split libraries according to barcodes specified in mapping file (split_libraries) 2
Split MAF blocks by Species 1
Split multisample OTUtable into a table persample 1
Split.abund Separate sequences into rare and abundant groups 6
Split.groups Generates a fasta file for each group 6
STAR-Fusion detect fusion genes in RNA-Seq data 5
staramr Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes. 6
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
Strelka detects somatic SNVs and small indels in tumour/normal pairs 1
Strip Header remove header from a file 1
Sub.sample Create a sub sample 6
Subset columns from a VCF dataset 1
SubtractBed remove intervals based on overlaps 16
Summarize taxa and store results in a new table or appended to an existing mapping file (summarize_taxa) 2
Summary Statistics for any numerical column 3
Summary.qual Summarize the quality scores 6
Summary.seqs Summarize the quality of sequences 6
Summary.shared Summary of calculator values for OTUs 5
Summary.single Summary of calculator values for OTUs 7
Summary.tax Assign sequences to taxonomy 6
tac reverse a file (reverse cat) 8
TagBed tag BAM alignments based on overlaps with interval files 16
Take an IGV screenshot specifying tracks and a genomic location 2
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 3
TestVariants Test for the presence of variants 3
TestVariants-2-VCF Convert CG MasterVar format to VCF format 2
Text reformatting with awk 7
Text transformation with sed 7
TITAN Estimate Cellular Prevalence and Call Copy Number Aberations 1
TopHat Gapped-read mapper for RNA-seq data 10
Transcript Integrity Number evaluates RNA integrity at a transcript level 5
transformVcfToCounts Tranform Mutationseq VCF to Counts 1
Transition Transversion Plot visualizes base change transitions and transversions 1
Transpose data from a file 1
Tree.shared Generate a newick tree for dissimilarity among groups 6
Trim leading or trailing characters 1
Trim Galore! Quality and adapter trimmer of reads 8
Trim.flows partition by barcode, trim to length, cull by length and mismatches 6
Trim.seqs Trim sequences - primers, barcodes, quality 6
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 14
Trinucleotide Signature Plots generate novel and known trinucleotide signatures for a cohort 1
Trioplot 1
twoBitToFa Convert all or part of .2bit file to FASTA 3
UNAFold UNAFold RNA and DNA structure prediction 1
Unfold columns from a table 7
Unified Genotyper SNP and indel caller 1
Unified Genotyper SNP and indel caller 3
unifrac.unweighted Describes whether two or more communities have the same structure 6
unifrac.weighted Describes whether two or more communities have the same structure 6
Unique occurrences of each record 8
Unique lines assuming sorted input file 7
Unique.seqs Return unique sequences 6
Upload File from your computer 2
Validate Variants 2
Validate Variants 1
ValidateSamFile assess validity of SAM/BAM dataset 12
VarFilter Copies input file, applying filters. 2
Variant Annotator 1
Variant Annotator 3
Variant Filtration on VCF files 3
Variant Filtration on VCF files 1
Variant Recalibrator 3
Variant Recalibrator 2
VarScan for variant detection 3
VarScan mpileup for variant detection 3
VarScan somatic Call germline/somatic and LOH variants from tumor-normal sample pairs 8
VarScan2 Call INDELs from a mpileup file VarScan2 INDEL detection (on mpileup data) 2
VarScan2 Call INDELs from BAM VarScan2 INDEL detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance. 2
VarScan2 Call SNPs from a mpileup file VarScan2 SNP/SNV detection; directly from a *.mpileup file. 2
VarScan2 Call SNPs from BAM VarScan2 SNP/SNV detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance. 2
VCF to ListVariants Convert a VCF file into a ListVariants file 2
VCF to MAF Custom Track for display at UCSC 2
VCF tools SlidingWindow Make diversity computation with sliding window 1
VCF-2-VariantList convert VCF file to CG-compatible variant list 1
VCF-BEDintersect: Intersect VCF and BED datasets 6
VCF-flatten Converts a VCF file to a tab-delimited file with one value per column 1
VCF-VCFintersect: Intersect two VCF datasets 7
vcf2maf Converts VCF files into MAF format 1
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 7
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 6
VCFannotate: Intersect VCF records with BED annotations 6
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 7
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 6
VCFcheck: Verify that the reference allele matches the reference genome 6
VCFcombine: Combine multiple VCF datasets 7
VCFcommonSamples: Output records belonging to samples common between two datasets 6
VCFdistance: Calculate distance to the nearest variant 6
VCFfilter: filter VCF data in a variety of attributes 7
VCFfixup: Count the allele frequencies across alleles present in each record in the VCF file 5
VCFflatten: Removes multi-allelic sites by picking the most common alternate 5
VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles 7
VCFgenotypes: Convert numerical representation of genotypes to allelic 6
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 6
VCFleftAlign: Left-align indels and complex variants in VCF dataset 6
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 7
VCFselectsamples: Select samples from a VCF dataset 7
VCFsort: Sort VCF dataset by coordinate 5
VCFtools Filter 1
VCFtools Stats 1
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 8
Venn Generate Venn diagrams for groups 6
Venn Diagram from summary counts 1
Virtual Normal Correction SmallVars Filter small variants based on presence in Virtual Normal set 1
Virtual Normal Correction SVs Filter SVs based on presence in VN set 1
Visualize with Krona Visualise any hierarchical data 2
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2
WindowBed find overlapping intervals within a window around an interval 16