392 tool(s) found

Tool Description Topics Available version(s)
ABySS de novo sequence assembler 2
Add column to an existing dataset 3
AddCommentsToBam add comments to BAM dataset 11
AddOrReplaceReadGroups add or replaces read group information 11
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 11
alignmentsieve Filter BAM/CRAM files according to specified parameters 5
alimask append modelmask line to a multiple sequence alignments 5
AnnotateBed annotate coverage of features from multiple files 17
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
BAM to BED converter 21
BAM-to-SAM convert BAM to SAM 8
bamCompare normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them 16
bamCoverage generates a coverage bigWig file from a given BAM file 16
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
Bar chart for multiple columns 1
Barcode Splitter 6
BED to BAM converter 18
BED to IGV create batch script for taking IGV screenshots 10
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 17
BedCov calculate read depth for a set of genomic intervals 4
BEDPE to BAM converter 18
BedToIntervalList convert coordinate data into picard interval list format 11
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
BlastAlign Align the nucleic acid sequences using BLASTN 1
Bowtie2 - map reads against reference genome 22
Boxplot of quality statistics 2
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 11
Busco assess genome assembly and annotation completeness 3
CalMD recalculate MD/NM tags 3
CDS_search ORF and CDS search 1
Change Case of selected columns 1
Choose Patterns of Interest in a Multiple Condition Design Choose patterns of interest in a multiple condition design 2
CleanSam perform SAM/BAM grooming 11
Clip adapter sequences 5
ClosestBed find the closest, potentially non-overlapping interval 17
ClusterBed cluster overlapping/nearby intervals 17
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
codeML Detects positive selection (paml package) 1
Collapse sequences 4
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 11
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 11
CollectGcBiasMetrics charts the GC bias metrics 11
CollectInsertSizeMetrics plots distribution of insert sizes 11
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 12
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 11
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 18
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 18
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 10
Compute quality statistics 4
computeGCBias Determine the GC bias of your sequenced reads 16
computeMatrix prepares data for plotting a heatmap or a profile of given regions 16
computeMatrixOperations Modify or combine the output of computeMatrix in a variety of ways. 9
Concatenate two datasets into one dataset Aggregation 6
Concatenate datasets tail-to-head 1
ConcatPhyl Concatenation and phylogeny 1
Convert delimiters to TAB 1
Convert BCF to BCF_BGZIP 1
Convert BCF to uncompressed BCF 1
Convert BCF_BGZIP to BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 1
Convert CSV to tabular 1
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 1
Convert FASTA to Tabular 1
Convert from BAM to FastQ 14
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 1
Convert SAM to BAM 1
Convert SAM to BAM without sorting 1
Convert tabular to CSV 1
Convert tabular to dbnsfp 1
Convert tar to directory 1
Convert uncompressed BCF to BCF 1
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Count occurrences of each record 2
Create single interval as a new dataset 1
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 14
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 13
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 11
Cuffmerge merge together several Cufflinks assemblies 12
Cuffnorm Create normalized expression levels 5
Cuffquant Precompute gene expression levels 5
Cut columns from a table 2
Data Fetch 1
Describe samples and replicates 9
DESeq2 Determines differentially expressed features from count tables Differential gene expression analysis 15
Diamond alignment tool for short sequences against a protein database 5
Diamond generate formatted output from DAA files 1
Diamond makedb Build database from a FASTA file 5
Differential expression analysis using a Trinity assembly 11
Download and Extract Reads in BAM format from NCBI SRA 12
Download and Extract Reads in FASTA/Q format from NCBI SRA 12
Download and Generate Pileup Format from NCBI SRA 11
Downsample SAM/BAM Downsample a file to retain a subset of the reads 11
Draw nucleotides distribution chart 4
Draw quality score boxplot 5
edgeR - Estimates differential gene expression for short read sequence count using methods appropriate for count data 2
EstimateLibraryComplexity assess sequence library complexity from read sequences 11
estimateReadFiltering estimates the number of reads that would be filtered given certain criteria 5
ExpandBed replicate lines based on lists of values in columns 17
Extract and cluster differentially expressed transcripts from a Trinity assembly 10
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
faSplit Split a FASTA file 2
FASTA Width formatter 4
fastp - fast all-in-one preprocessing for FASTQ files 5
FASTQ Groomer convert between various FASTQ quality formats 4
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 5
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 17
FastqToSam convert Fastq data into unaligned BAM 14
Filter data on any column using simple expressions Formatting 1
Filter assemblies Filter the outputs of Velvet or Trinity assemblies 1
Filter by quality 5
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 low expression transcripts from a Trinity assembly 11
Filter SAM on bitwise flag values 2
Filter sequences by ID from a tabular file 5
Filter sequences by length Filtering 5
Filter with SortMeRNA Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data 6
FilterSamReads include or exclude aligned and unaligned reads and read lists 11
FisherBed calculate Fisher statistic between two feature files 17
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 11
Flagstat tabulate descriptive stats for BAM datset 8
FlankBed create new intervals from the flanks of existing intervals 18
GATK 3 tool collection Version 3.5-0 1
Gene BED To Exon/Intron/Codon BED expander 1
Gene level DE test across multiple conditions Runs EBSeq to find DE genes across multiple (more than two) conditions 2
Gene level DE test across two conditions Runs EBSeq to find DE genes across two conditions 2
Generate gene to transcript map for Trinity assembly 11
Generate SuperTranscripts from a Trinity assembly 5
Genome Coverage compute the coverage over an entire genome 18
Get All Possible Patterns in a Multiple Condition Design Get all possible patterns in a multiple condition design 2
Get Ig vector from gene-isoform mapping for isoform level DE analysis Get Ig vector from gene-isoform mapping for isoform level DE analysis 2
Get Microbial Data 1
Get Normalized Expressions Calculate normalization factors and get the normalized expression matrix 2
GetFastaBed use intervals to extract sequences from a FASTA file 17
GFF-to-BED converter Conversion 1
GffCompare compare assembled transcripts to a reference annotation 2
gffread Filters and/or converts GFF3/GTF2 records 3
Group data by a column and perform aggregate operation on other columns. 3
GroupByBed group by common cols and summarize other cols 17
GTF-to-BEDGraph converter Conversion 1
Heatmap Heatmap of the dataMatrix 3
heatmap2 4
HISAT2 A fast and sensitive alignment program 16
hmmalign align sequences to a profile HMM 5
hmmbuild Build a profile HMM from an input multiple alignment 5
hmmconvert convert profile file to a HMMER format 5
hmmemit sample sequence(s) from a profile HMM 5
hmmfetch retrieve profile HMM(s) from a file 5
hmmscan search sequence(s) against a profile database 5
hmmsearch search profile(s) against a sequence database 5
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
IdxStats tabulate mapping statistics for BAM dataset 9
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Intersect the intervals of two datasets Filtering 7
Intersect intervals find overlapping intervals in various ways 17
Isoform level DE test across multiple conditions Runs EBSeq to find DE isoforms across multiple (more than two) conditions 2
Isoform level DE test across two conditions Runs EBSeq to find DE isoforms across two conditions 2
JaccardBed calculate the distribution of relative distances between two files 17
jackhmmer iteratively search a protein sequence against a protein database (PSIBLAST-like) 5
Join the intervals of two datasets side-by-side Aggregation 5
Join two Datasets side by side on a specified field 3
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 2
Kallisto quant - quantify abundances of RNA-Seq transcripts 4
LAV to BED Converts a LAV formatted file to BED format 1
Length Distribution chart 3
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 17
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 9
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 8
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 11
MACS2 filterdup Remove duplicate reads at the same position Regulatory element prediction 8
MACS2 predictd Predict 'd' or fragment size from alignment results Regulatory element prediction 8
MACS2 randsample Randomly sample number or percentage of total reads Regulatory element prediction 8
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) Regulatory element prediction 8
Maker genome annotation pipeline 3
MakeWindowsBed make interval windows across a genome 18
Map annotation ids on a Maker annotation 3
Map with Bowtie for Illumina 8
Map with BWA - map short reads (< 100 bp) against reference genome 15
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 17
MapBed apply a function to a column for each overlapping interval 17
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 11
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 11
MaskFastaBed use intervals to mask sequences from a FASTA file 17
MeanQualityByCycle chart distribution of base qualities 11
Merge the overlapping intervals of a dataset Sequence merging 5
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 17
Merge Columns together 2
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 11
MergeBED combine overlapping/nearby intervals into a single interval 17
MergeSamFiles merges multiple SAM/BAM datasets into one 11
MIRA v4.0 de novo assember Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads 1
MIRA v4.0 mapping Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads 1
MIRA v4.0 mirabait Filter reads using kmer matches 1
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
MPileup call variants 10
multiBamSummary calculates average read coverages for a list of two or more BAM/CRAM files 17
multiBigwigSummary calculates average scores for a list of two or more bigwig files 17
MultiCovBed counts coverage from multiple BAMs at specific intervals 17
Multiple Intersect identifies common intervals among multiple interval files 21
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 9
MutCount This tool proceeds to count codons, amino acids on each species of a set of species, and then proceeds to permutation tests. 1
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 12
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 10
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 12
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
nhmmer search a DNA model or alignment against a DNA database (BLASTN-like) 5
nhmmscan search DNA sequence(s) against a DNA profile database 5
NormalizeFasta normalize fasta datasets 11
NucBed profile the nucleotide content of intervals in a FASTA file 17
Oligator Oligator: design PCR primers 1
OrthoFinder OnlyGroups finds orthogroups in a set of proteomes 1
Orthogroups_Tool Writes orthogroups found by OrthoFinder in fasta files (with their sequences). 1
OverlapBed computes the amount of overlap from two intervals 17
Pairwise Find homologous couples by blast with RBH 1
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 10
Paste two files side by side 1
Pear Paired-End read merger 4
phmmer search a protein sequence against a protein database (BLASTP-like) 5
Phyogenetic reconstruction with RaXML - Maximum Likelihood based inference of large phylogenetic trees 3
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 16
plotCoverage assesses the sequencing depth of BAM/CRAM files 16
plotEnrichment plots read/fragment coverage over sets of regions 12
plotFingerprint plots profiles of BAM files; useful for assessing ChIP signal strength 16
plotHeatmap creates a heatmap for score distributions across genomic regions 17
plotPCA Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output 16
plotProfile creates a profile plot for score distributions across genomic regions 16
POGs Find orthologous groups 1
Preprocess files for SARTools generate design/target file and archive for SARTools inputs 5
PRINSEQ to process quality of sequences 3
Quality format converter (ASCII-Numeric) 4
QualityScoreDistribution chart quality score distribution 11
RandomBed generate random intervals in a genome 18
Reheader copy SAM/BAM header between datasets 2
ReldistBed calculate the distribution of relative distances 17
Remove beginning of a file 1
Remove sequencing artifacts 5
Rename sequences 5
ReorderSam reorder reads to match ordering in reference sequences 14
RepeatMasker RepeatMasker 4
ReplaceSamHeader replace header in a SAM/BAM dataset 14
Reverse-Complement 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 11
RevertSam revert SAM/BAM datasets to a previous state 11
RmDup remove PCR duplicates 8
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly 11
RNA/DNA converter 5
RNASeq samples quality check for transcript quantification 11
RSEM calculate expression RNA-Seq by Expectation-Maximization 1
RSEM prepare reference 1
RSEM trinity fasta to gene map extract transcript to gene map from trinity 2
Salmon Transcript Quantification from RNA-seq data 5
SAM-to-BAM convert SAM to BAM 11
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 14
Samtools view reformat, filter, or subsample 2
SARTools DESeq2 Compare two or more biological conditions in a RNA-Seq framework with DESeq2 6
SARTools edgeR Compare two or more biological conditions in a RNA-Seq framework with edgeR 5
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Secure Hash / Message Digest on a dataset 1
Select lines that match an expression 1
Select first lines from a dataset 1
Select last lines from a dataset 1
Select random lines from a file 2
SFF converter 1
ShuffleBed randomly redistrubute intervals in a genome 18
Sickle windowed adaptive trimming of FASTQ data 5
SignalP 3.0 Find signal peptides in protein sequences 3
Slice BAM by genomic regions 6
SlopBed adjust the size of intervals 18
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
SnpEff Variant effect and annotation 15
SnpEff Available Databases 11
SnpEff Download Download a new database 15
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift dbNSFP Add Annotations from dbNSFP or similar annotation DBs 4
SnpSift Extract Fields from a VCF file inot a tabular file 6
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 9
SnpSift rmInfo remove INFO field annotations 7
SnpSift Variant Type Annotate with variant type 7
SnpSift vcfCheck basic checks for Vcf specification compliance 7
Sort BAM dataset 8
Sort data in ascending or descending order 2
SortBED order the intervals 17
SortSam sort SAM/BAM dataset 11
SpacingBed reports the distances between features 13
SPAdes genome assembler for regular and single-cell projects 10
Split BAM dataset on readgroups 3
Stacks: assemble read pairs by locus run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers 3
Stacks: clone filter Identify PCR clones 1
Stacks: cstacks build a catalogue of loci 4
Stacks: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 4
Stacks: genotypes analyse haplotypes or genotypes in a genetic cross ('genotypes' program) 3
Stacks: populations analyze a population of individual samples ('populations' program) 3
Stacks: process radtags the Stacks demultiplexing script 3
Stacks: pstacks find stacks from short reads mapped to a reference genome 3
Stacks: reference map the Stacks pipeline with a reference genome (ref_map.pl) 3
Stacks: rxstacks make corrections to genotype and haplotype calls 3
Stacks: sstacks match stacks to a catalog 3
Stacks: statistics on stacks found for multiple samples 1
Stacks: ustacks align short reads into stacks 3
Stats generate statistics for BAM dataset 5
StringTie transcript assembly and quantification 13
StringTie merge transcripts 7
Structure using multi-locus genotype data to investigate population structure 3
structureHarvester for parsing STRUCTURE outputs and for performing the Evanno method 1
Subtract the intervals of two datasets Filtering 7
SubtractBed remove intervals based on overlaps 17
Summary Statistics for any numerical column 3
TagBed tag BAM alignments based on overlaps with interval files 17
TMHMM 2.0 Find transmembrane domains in protein sequences 4
TopHat Gapped-read mapper for RNA-seq data 12
TopHat for Illumina Find splice junctions using RNA-seq data 3
TransDecoder Find coding regions within transcripts 4
Transpose rows/columns in a tabular file 3
Trim leading or trailing characters 1
Trim sequences 6
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 13
Trinity de novo assembly of RNA-Seq data 13
Trinity Statistics Obtain basic stats for the number of genes and isoforms and contiguity of the assembly 1
Trinotate 2
Upload File from your computer 2
ValidateSamFile assess validity of SAM/BAM dataset 11
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1
WindowBed find overlapping intervals within a window around an interval 17