661 tool(s) found

Tool Description Topics Available version(s)
ABRicate 3
ABRicate List 3
Add column to an existing dataset 3
AddCommentsToBam add comments to BAM dataset 9
AddOrReplaceReadGroups add or replaces read group information 9
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 8
Analyse canonical genes against 'peak' data using RnaChipIntegrator 3
Annotate a VCF dataset with custom filters 2
Annotate a VCF file (dbSNP, hapmap) 1
AnnotateBed annotate coverage of features from multiple files 16
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 3
Apply Variant Recalibration 4
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
backtranseq Back translate a protein sequence 4
BAM filter Removes reads from a BAM file based on criteria 4
BAM to BED converter 20
BAM to fastq Convert BAM file to fastq 1
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 8
BAM-to-SAM convert BAM to SAM 7
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 8
bamCompare normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them 14
bamCoverage generates a coverage bigWig file from a given BAM file 14
BamLeftAlign indels in BAM datasets 7
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM files 14
banana Bending and curvature plot in B-DNA 4
Bar chart for multiple columns 1
Barcode Splitter 5
barrnap Locate ribosomal RNA's in a fasta file. (GFF output) 1
Base Coverage of all intervals Quantification 5
Base Recalibrator calculates covariates used to recalibrate base quality scores of reads 4
bcftools annotate Annotate and edit VCF/BCF files 2
bcftools call SNP/indel variant calling from VCF/BCF 6
bcftools cnv Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR) 2
bcftools concat Concatenate or combine VCF/BCF files 2
bcftools consensus Create consensus sequence by applying VCF variants to a reference fasta file 2
bcftools convert from vcf Converts VCF/BCF to IMPUTE2/SHAPEIT formats 2
bcftools convert to vcf Converts other formats to VCF/BCFk 2
bcftools counts plugin counts number of samples, SNPs, INDELs, MNPs and total sites 2
bcftools csq Haplotype aware consequence predictor 2
bcftools dosage plugin genotype dosage 2
bcftools fill-AN-AC plugin Fill INFO fields AN and AC 2
bcftools fill-tags plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi 2
bcftools filter Apply fixed-threshold filters 2
bcftools fixploidy plugin Fix ploidy 2
bcftools gtcheck Check sample identity 2
bcftools impute-info plugin Add imputation information metrics to the INFO field 2
bcftools isec Create intersections, unions and complements of VCF files 2
bcftools List Samples in VCF/BCF file 2
bcftools mendelian plugin Count Mendelian consistent / inconsistent genotypes 2
bcftools merge Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file 2
bcftools missing2ref plugin Set missing genotypes 2
bcftools mpileup Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files 2
bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows 2
bcftools query Extracts fields from VCF/BCF file and prints them in user-defined format 2
bcftools reheader Modify header of VCF/BCF files, change sample names 2
bcftools roh HMM model for detecting runs of homo/autozygosity 2
bcftools setGT plugin Sets genotypes 2
bcftools stats Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats 2
bcftools tag2tag plugin Convert between similar tags, such as GL and GP 2
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 9
BED to BAM converter 17
BED to IGV create batch script for taking IGV screenshots 9
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 16
BED_to_GFF3 converter 3
BedCov calculate read depth for a set of genomic intervals 3
BEDPE to BAM converter 17
BedToIntervalList convert coordinate data into picard interval list format 9
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 14
BIOM metadata add-metadata Conversion Format validation 2
biosed Replace or delete sequence sections 4
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 15
Bowtie2 - map reads against reference genome 21
Boxplot of quality statistics 1
btwisted Calculates the twisting in a B-DNA sequence 4
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 8
Bundle Collection Download a collection of files 1
Busco assess genome assembly and annotation completeness 3
cai CAI codon adaptation index 4
cai custom CAI codon adaptation index using custom codon usage file 4
Call and phase heterozygous SNPs 4
CalMD recalculate MD/NM tags 2
Categorize Elements satisfying criteria 2
Change Case of selected columns 1
chaos Create a chaos game representation plot for a sequence 4
charge Protein charge plot 3
checktrans Reports STOP codons and ORF statistics of a protein 3
chips Codon usage statistics 4
Circos Builder creates circos plots from standard bioinformatics datatypes. 2
cirdna Draws circular maps of DNA constructs 4
CleanSam perform SAM/BAM grooming 9
Clip adapter sequences 5
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 8
ClosestBed find the closest, potentially non-overlapping interval 16
ClustalW multiple sequence alignment program for DNA or proteins 4
Cluster the intervals of a dataset Sequence clustering Sequence merging 5
Cluster OTU Cluster OTUs 1
ClusterBed cluster overlapping/nearby intervals 16
cmalign Align sequences to a covariance model against a sequence database 2
cmbuild Build covariance models from sequence alignments 3
CML to InChI 2
CML to mol2 2
CML to SDF 2
cmpress Prepare a covariance model database for cmscan 1
cmscan Search sequences against collections of covariance models 1
cmsearch Search covariance model(s) against a sequence database 2
cmstat Summary statistics for covariance model 2
codcmp Codon usage table comparison 4
coderet Extract CDS, mRNA and translations from feature tables 4
Collapse sequences 4
Collapse Collection into single dataset in order of the collection 3
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 9
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 9
CollectGcBiasMetrics charts the GC bias metrics 9
CollectInsertSizeMetrics plots distribution of insert sizes 9
Collector Curve Calculate and plot collector's curves for OTUs 6
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 10
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 9
Column Join on Collections 3
Column Regex Find And Replace 3
Combine FASTA and QUAL into FASTQ 3
Combine Variants 4
Compare two Datasets to find common or distinct rows 1
Complement intervals of a dataset Sequence coordinate conversion 6
ComplementBed Extract intervals not represented by an interval file 17
compseq Count composition of dimer/trimer/etc words in a sequence 3
Compute an expression on every row 3
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 17
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 7
Compute Motif Frequencies in indel flanking regions 2
Compute Motif Frequencies For All Motifs motif by motif 2
Compute P-values and Correlation Coefficients for Feature Occurrences between two datasets using Discrete Wavelet Transfoms 1
Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features between two datasets using Discrete Wavelet Transfoms 1
Compute P-values and Max Variances for Feature Occurrences in one dataset using Discrete Wavelet Transfoms 1
Compute P-values and Second Moments for Feature Occurrences between two datasets using Discrete Wavelet Transfoms 1
Compute quality statistics 4
Compute sequence length 4
computeGCBias Determine the GC bias of your sequenced reads 14
computeMatrix prepares data for plotting a heatmap or a profile of given regions 14
computeMatrixOperations Modify or combine the output of computeMatrix in a variety of ways. 8
Concatenate two datasets into one dataset Aggregation 6
Concatenate FASTA alignment by species 2
Concatenate datasets tail-to-head 1
Concatenate multiple datasets tail-to-head 1
Condense consecutive characters 2
Convert delimiters to TAB 1
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert BIOM formats 1
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 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 interval 2
Convert SAM to BAM without sorting 1
Convert tabular to dbnsfp 1
Convert uncompressed BCF to BCF 1
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM files 14
Correlation for numeric columns 2
Count occurrences of each record 1
Count GFF Features 3
Coverage of a set of intervals on second set of intervals Comparison Filtering 5
cpgplot Plot CpG rich areas 4
cpgreport Reports all CpG rich regions 3
Create assemblies with Unicycler 6
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
cummeRbund visualize Cuffdiff output 3
cusp Create a codon usage table 4
Cut columns from a table 2
Cutadapt Remove adapter sequences from Fastq/Fasta 12
cutseq Removes a specified section from a sequence 3
dan Calculates DNA RNA/DNA melting temperature 3
Data Fetch 1
Datamash (operations on tabular data) 3
degapseq Removes gap characters from sequences 4
Deletion Profile calculates the distributions of deleted nucleotides across reads 2
Depth of Coverage on BAM files 4
Dereplicate Remove duplicate sequences 1
Describe samples and replicates 6
descseq Alter the name or description of a sequence 4
DESeq2 Determines differentially expressed features from count tables Differential gene expression analysis 14
DEXSeq Determines differential exon usage from count tables 4
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 4
DiffBind differential binding analysis of ChIP-Seq peak data 11
Differential expression analysis using a Trinity assembly 8
Differential_Count models using BioConductor packages 1
diffseq Find differences between nearly identical sequences 3
digest Protein proteolytic enzyme or reagent cleavage digest 4
dotmatcher Displays a thresholded dotplot of two sequences 3
dotpath Non-overlapping wordmatch dotplot of two sequences 3
dottup Displays a wordmatch dotplot of two sequences 3
Downsample SAM/BAM Downsample a file to retain a subset of the reads 9
Draw nucleotides distribution chart 4
Draw quality score boxplot 5
Draw ROC plot on "Perform LDA" output 3
Draw Stacked Bar Plots for different categories and different criteria 2
dreg Regular expression search of a nucleotide sequence 4
edgeR Perform differential expression of count data 3
einverted Finds DNA inverted repeats 3
epestfind Finds PEST motifs as potential proteolytic cleavage sites 3
equicktandem Finds tandem repeats 3
est2genome Align EST and genomic DNA sequences 3
Estimate substitution rates for non-coding regions 2
EstimateLibraryComplexity assess sequence library complexity from read sequences 9
etandem Looks for tandem repeats in a nucleotide sequence 3
Eval Variants 4
ExpandBed replicate lines based on lists of values in columns 16
eXpress Quantify the abundances of a set of target sequences from sampled subsequences 2
Extract reads from a specified region 1
Extract and cluster differentially expressed transcripts from a Trinity assembly 7
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
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 Pairwise MAF blocks given a set of genomic intervals 1
Extract reads in FASTQ/A format from NCBI SRA. 11
Extract reads in SAM format from NCBI SRA. 11
extractfeat Extract features from a sequence 3
extractseq Extract regions from a sequence 4
Fasta Extract Sequence Extract a single sequence from a fasta file. 1
Fasta Statistics Display summary statistics for a fasta file. 1
FASTA Width formatter 4
FASTA-to-Tabular converter 3
FASTQ de-interlacer on paired end reads 3
FASTQ Groomer convert between various FASTQ quality formats 4
FASTQ interlacer on paired end reads 4
FASTQ joiner on paired end reads 6
FASTQ Masker by quality score 3
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads 3
FASTQ Summary Statistics by column 2
FASTQ to FASTA converter Sequence conversion 5
FASTQ to Tabular converter 4
FASTQ Trimmer by column 4
FastQC:Read QC reports using FastQC Sequence composition calculation Sequencing quality control Statistical calculation 16
FastqToSam convert Fastq data into unaligned BAM 12
FASTTREE adjust short reads Phylogenetic tree analysis Phylogenetic tree generation (from molecular sequences) 4
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 15
Fetch closest non-overlapping feature for every interval Filtering 4
Filter a VCF file 2
Filter data on any column using simple expressions Formatting 1
Filter by quality 5
Filter Combined Transcripts using tracking file 1
Filter FASTQ reads by quality score and length 4
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 8
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
Filter pileup on coverage and SNPs 3
Filter SAM on bitwise flag values 2
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 5
Filter sequences by length Filtering 5
FilterSamReads include or exclude aligned and unaligned reads and read lists 9
FisherBed calculate Fisher statistic between two feature files 16
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 9
Flagstat tabulate descriptive stats for BAM datset 7
FlankBed create new intervals from the flanks of existing intervals 17
FPKM Count calculates raw read count, FPM, and FPKM for each gene 4
freak Residue/base frequency table or plot 3
FreeBayes bayesian genetic variant detector 7
fuzznuc Nucleic acid pattern search 4
fuzzpro Protein pattern search 3
fuzztran Protein pattern search after translation 3
garnier Predicts protein secondary structure 4
GBK-to-GFF converter 2
geecee Calculates fractional GC content of nucleic acid sequences 4
Genbank-to-Fasta produces a Fasta file from a genbank file 1
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Converage (BAM) Read coverage over gene body. 11
Gene Body Converage (Bigwig) Read coverage over gene body 10
Generate A Matrix for using PC and LDA 2
Generate count matrix from individual files 1
Generate gene to transcript map for Trinity assembly 8
Generate pileup from BAM dataset 3
Generate pileup format from NCBI sra. 10
Genome Coverage compute the coverage over an entire genome 17
Get flanks returns flanking region/s for every gene Sequence analysis 5
Get Microbial Data 1
GetFastaBed use intervals to extract sequences from a FASTA file 16
getorf Finds and extracts open reading frames (ORFs) 3
GFF-to-BED converter Conversion 1
GFF-to-BED converter 2
GFF-to-GTF converter 1
GffCompare compare assembled transcripts to a reference annotation 1
GMAJ Multiple Alignment Viewer 1
Group data by a column and perform aggregate operation on other columns. 2
GroupByBed group by common cols and summarize other cols 16
GTF-to-BEDGraph converter Conversion 1
GTF-to-GFF converter 1
Gubbins Recombination detection in Bacteria 1
Haplotype Caller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region 3
helixturnhelix Report nucleic acid binding motifs 3
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 2
HISAT2 A fast and sensitive alignment program 14
Histogram of a numeric column 4
hmoment Hydrophobic moment calculation 3
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
IDR Consistency Analysis on a pair of narrowPeak files 1
IDR-Plot Plot Consistency Analysis on IDR output files 1
IdxStats tabulate mapping statistics for BAM dataset 8
iep Calculates the isoelectric point of a protein 3
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
Indel Realigner - perform local realignment 4
Infer Experiment speculates how RNA-seq were configured 10
infoseq Displays some simple information about sequences 4
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 10
Insertion Profile calculates the distribution of inserted nucleotides across reads 2
Intersect Generate the intersection of two VCF files 2
Intersect the intervals of two datasets Filtering 7
Intersect multiple VCF datasets 3
Intersect intervals find overlapping intervals in various ways 16
Intersect multiple sorted BED files 20
isochore Plots isochores in large DNA sequences 3
JaccardBed calculate the distribution of relative distances between two files 16
JBrowse genome browser 11
JBrowse - Data Directory to Standalone upgrades the bare data directory to a full JBrowse instance 7
Join the intervals of two datasets side-by-side Aggregation 5
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 2
Junction Annotation compares detected splice junctions to reference gene model 10
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 10
KmerGenie k-mer histograms analysis 2
Kraken assign taxonomic labels to sequencing reads 5
Kraken-filter filter classification by confidence score 3
Kraken-mpa-report view report of classification for multiple samples 5
Kraken-report view sample report of a classification 4
Kraken-translate convert taxonomy IDs to names 3
Lastz map short reads against reference sequence 5
Lastz paired reads map short paired reads against reference sequence 2
LAV to BED Converts a LAV formatted file to BED format 1
Length Distribution chart 3
lindna Draws linear maps of DNA constructs 3
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 16
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 7
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 7
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 8
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 7
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 10
MACS2 filterdup Remove duplicate reads at the same position Regulatory element prediction 7
MACS2 predictd Predict 'd' or fragment size from alignment results Regulatory element prediction 7
MACS2 randsample Randomly sample number or percentage of total reads Regulatory element prediction 7
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) Regulatory element prediction 7
MACS2.1.1 Model-based Analysis of ChIP-Seq: peak calling 1
MAF Coverage Stats Alignment coverage information 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
MakeWindowsBed make interval windows across a genome 17
Manipulate FASTQ reads on various attributes 3
Map Reads to OTU Maps read sequences to OTUs 1
Map with BWA - map short reads (< 100 bp) against reference genome 14
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 16
MapBed apply a function to a column for each overlapping interval 16
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 9
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 9
marscan Finds MAR/SAR sites in nucleic sequences 4
MaskFastaBed use intervals to mask sequences from a FASTA file 16
maskfeat Mask off features of a sequence 4
maskseq Mask off regions of a sequence 4
matcher Finds the best local alignments between two sequences 3
MeanQualityByCycle chart distribution of base qualities 9
megamerger Merge two large overlapping nucleic acid sequences 3
Merge the overlapping intervals of a dataset Sequence merging 5
Merge multiple VCF datasets 3
Merge BAM Files merges BAM files together 3
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 16
Merge Columns together 2
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 9
MergeBED combine overlapping/nearby intervals into a single interval 16
merger Merge two overlapping nucleic acid sequences 3
MergeSamFiles merges multiple SAM/BAM datasets into one 9
Mismatch Profile calculates the distribution of mismatches across reads 2
MLST List 1
MOL to CML 2
MOL to MOL2 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MPileup call variants 10
msbar Mutate sequence beyond all recognition 3
multiBamSummary calculates average read coverages for a list of two or more BAM files 15
multiBigwigSummary calculates average scores for a list of two or more bigwig files 15
MultiCovBed counts coverage from multiple BAMs at specific intervals 16
multiqc aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 8
MUMmer dotplot Combine mummer/nucmer/promer with mummerplot 4
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 15
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 11
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 15
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 13
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 16
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 9
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 14
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 14
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 11
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
needle Needleman-Wunsch global alignment 3
newcpgreport Report CpG rich areas 3
newcpgseek Reports CpG rich region 3
newseq Type in a short new sequence 4
noreturn Removes carriage return from ASCII files 4
NormalizeFasta normalize fasta datasets 9
notseq Exclude a set of sequences and write out the remaining ones 4
nthseq Writes one sequence from a multiple set of sequences 3
NucBed profile the nucleotide content of intervals in a FASTA file 16
octanol Displays protein hydropathy 3
oddcomp Find protein sequence regions with a biased composition 3
OverlapBed computes the amount of overlap from two intervals 16
palindrome Looks for inverted repeats in a nucleotide sequence 3
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 7
Paste two files side by side 1
pasteseq Insert one sequence into another 3
patmatdb Search a protein sequence with a motif 4
Pear Paired-End read merger 4
pepcoil Predicts coiled coil regions 3
pepinfo Plots simple amino acid properties in parallel 3
pepnet Displays proteins as a helical net 4
pepstats Protein statistics 4
pepwheel Shows protein sequences as helices 3
pepwindow Displays protein hydropathy 3
pepwindowall Displays protein hydropathy of a set of sequences 3
Pileup-to-Interval condenses pileup format into ranges of bases 5
pilon An automated genome assembly improvement and variant detection tool 2
plotcon Plot quality of conservation of a sequence alignment 3
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 14
plotCoverage assesses the sequencing depth of BAM files 14
plotEnrichment plots read/fragment coverage over sets of regions 10
plotFingerprint plots profiles of BAM files; useful for assesing ChIP signal strength 14
plotHeatmap creates a heatmap for score distributions across genomic regions 15
plotorf Plot potential open reading frames 4
plotPCA Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output 14
plotProfile creates a profile plot for score distributions across genomic regions 14
Plotting tool for multiple series and graph types 4
Poisson two-sample test 1
polydot Displays all-against-all dotplots of a set of sequences 3
preg Regular expression search of a protein sequence 4
prettyplot Displays aligned sequences, with colouring and boxing 3
prettyseq Output sequence with translated ranges 3
primersearch Searches DNA sequences for matches with primer pairs 3
Print Reads on BAM files 4
Profile Annotations for a set of genomic intervals 2
Prokka Prokaryotic genome annotation 5
proportional venn from 2-3 sets 1
PyNAST PyNAST is a reimplementation of the NAST sequence aligner for adding new 16S rDNA sequences to existing 16S rDNA alignments. 1
Quality format converter (ASCII-Numeric) 4
QualityScoreDistribution chart quality score distribution 9
Quast Genome assembly Quality 4
RandomBed generate random intervals in a genome 17
Rarefaction Calculate and plot rarefaction curves 1
raxml Maximum Likelihood Analysis 3
RDP MultiClassifier Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy 1
Read Distribution calculates how mapped reads were distributed over genome feature 10
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 8
Read GC determines GC% and read count 8
Read NVC to check the nucleotide composition bias 8
Read Quality determines Phred quality score 8
Realigner Target Creator for use in local realignment 4
Reduce Reads in BAM files 4
Regex Find And Replace 2
Reheader copy SAM/BAM header between datasets 2
ReldistBed calculate the distribution of relative distances 16
Remove beginning of a file 1
Remove sequencing artifacts 5
Rename sequences 5
ReorderSam reorder reads to match ordering in reference sequences 12
ReplaceSamHeader replace header in a SAM/BAM dataset 12
Reverse Complement a MAF file 1
Reverse-Complement 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 9
RevertSam revert SAM/BAM datasets to a previous state 9
revseq Reverse and complement a sequence 4
RmDup remove PCR duplicates 7
RNA fragment size calculates the fragment size for each gene/transcript 4
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly 9
RNA/DNA converter 5
RnaChipIntegrator Integrated analysis of 'gene' and 'peak' data 3
RNASeq samples quality check for transcript quantification 8
Roary the pangenome pipeline - Quickly generate a core gene alignment from gff3 files 2
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 10
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
Sailfish transcript quantification from RNA-seq data 4
Salmon Transcript Quantification from RNA-seq data 4
SAM-to-BAM convert SAM to BAM 10
SAM/BAM to count matrix using HTSeq code 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 12
SDF to CML 2
SDF to InChI 2
SDF to mol2 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
Select sequences by ID from a tabular file 3
Select Variants from VCF files 4
seqmatchall All-against-all comparison of a set of sequences 3
seqret Reads and writes sequences 4
Sequence Logo Generator from fasta 3
SFF converter 1
Shovill Faster SPAdes assembly of Illumina reads 2
showfeat Show features of a sequence 3
ShuffleBed randomly redistrubute intervals in a genome 17
shuffleseq Shuffles a set of sequences maintaining composition 3
SICER Statistical approach for the Identification of ChIP-Enriched Regions 1
sigcleave Reports protein signal cleavage sites 3
sirna Finds siRNA duplexes in mRNA 4
sixpack Display a DNA sequence with 6-frame translation and ORFs 4
skipseq Reads and writes sequences, skipping first few 3
Slice BAM by genomic regions 6
Slice VCF to get data from selected regions 2
SlopBed adjust the size of intervals 17
snippy Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 1
snippy-core Combine multiple Snippy outputs into a core SNP alignment 1
SNP splitter splits multicharacter entries into separate lines 1
SNP table merger merges any number of SNP tables into one 1
SnpEff Variant efefct and annotation 14
SnpEff available databases 10
SnpEff Download Download a new database 14
snpFreq significant SNPs in case-control data 3
SnpSift Annotate Annotate SNPs from dbSnp 8
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 8
SnpSift Extract Fields from a VCF file into a tabular file 5
SnpSift Filter Filter variants using arbitrary expressions 8
SnpSift Intervals Filter variants using intervals 8
SnpSift rmInfo remove INFO field annotations 6
SnpSift Variant Type Annotate with variant type 6
SnpSift vcfCheck basic checks for Vcf specification compliance 6
Sort BAM dataset 7
Sort data in ascending or descending order 2
SortBED order the intervals 16
SortSam sort SAM/BAM dataset 9
SpacingBed reports the distances between features 12
spades SPAdes genome assembler for regular and single-cell projects 9
Split BAM dataset on readgroups 2
Split MAF blocks by Species 1
Split paired end reads 2
splitter Split a sequence into (overlapping) smaller sequences 3
SPP SPP cross-correlation analysis package 1
Stats generate statistics for BAM dataset 4
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 12
StringTie merge transcripts 6
Subset columns from a VCF dataset 2
Subtract the intervals of two datasets Filtering 7
Subtract Whole Dataset from another dataset 3
SubtractBed remove intervals based on overlaps 16
Summary Statistics for any numerical column 3
supermatcher Match large sequences against one or more other sequences 3
syco Synonymous codon usage Gribskov statistic plot 3
T Test for Two Samples 2
Tabular to FASTQ converter 4
Tabular-to-FASTA converts tabular file to FASTA format 2
TagBed tag BAM alignments based on overlaps with interval files 16
tcode Fickett TESTCODE statistic to identify protein-coding DNA 3
textsearch Search sequence documentation. Slow, use SRS and Entrez! 4
tmap Displays membrane spanning regions 4
TopHat Gapped-read mapper for RNA-seq data 12
Tophat Fusion Post post-processing to identify fusion genes 1
TRAMS Tool for Rapid Annotation of Microbial SNPs 1
tranalign Align nucleic coding regions given the aligned proteins 4
Transcript Integrity Number evaluates RNA integrity at a transcript level 4
TransDecoder Find coding regions within transcripts 4
transeq Translate nucleic acid sequences 4
Trim leading or trailing characters 1
Trim Galore! Quality and adapter trimmer of reads 7
Trim sequences 6
trimest Trim poly-A tails off EST sequences 3
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 11
trimseq Trim ambiguous bits off the ends of sequences 3
Trinity De novo assembly of transcriptome from RNA-Seq data 10
Trinotate 2
twofeat Finds neighbouring pairs of features in sequences 3
Uchime Detecting chimeric sequences with two or more segments. 1
Unified Genotyper SNP and indel caller 4
union Reads sequence fragments and builds one sequence 4
Upload File from your computer 2
Validate Variants 3
ValidateSamFile assess validity of SAM/BAM dataset 9
Variant Annotator 4
Variant Filtration on VCF files 4
Variant Recalibrator 4
Varscan for variant detection 3
VCF to MAF Custom Track for display at UCSC 1
vectorstrip Strips out DNA between a pair of vector sequences 3
velvet 1
velvetoptimiser Auto optimise a genomic velvet assembly 4
Visualize with Krona Visualise any hierarchical data 2
VSearch alignment Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch chimera detection Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch clustering Chimeric sequence detection Sequence clustering Sequence masking 6
VSearch dereplication Chimeric sequence detection Sequence clustering Sequence masking 6
VSearch masking Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch search Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch shuffling Chimeric sequence detection Sequence clustering Sequence masking 5
VSearch sorting Chimeric sequence detection Sequence clustering Sequence masking 6
water Smith-Waterman local alignment 3
Wavelet variance using Discrete Wavelet Transfoms 2
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 16
wobble Wobble base plot 3
wordcount Counts words of a specified size in a DNA sequence 3
wordmatch Finds all exact matches of a given size between 2 sequences 3