Add column |
to an existing dataset |
|
3 |
Add input name as column |
to an existing tabular file |
|
2 |
AddCommentsToBam |
add comments to BAM dataset |
|
12 |
AddOrReplaceReadGroups |
add or replaces read group information |
|
12 |
AnnotateBed |
annotate coverage of features from multiple files |
|
17 |
AnnotatePeaks |
Genomic annotation of Chip-Seq peaks |
|
2 |
Apply Variant Recalibration |
|
|
3 |
Arithmetic Operations |
on tables |
|
2 |
BAM to BED |
converter |
|
19 |
BAM-to-SAM |
convert BAM to SAM |
|
7 |
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 |
|
17 |
bamPEFragmentSize |
Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files |
|
16 |
Base Coverage |
of all intervals |
Quantification
|
5 |
Base Recalibrator |
calculates covariates used to recalibrate base quality scores of reads |
|
3 |
bcftools call |
SNP/indel variant calling from VCF/BCF |
|
9 |
bcftools view |
Converts BCF format to VCF format |
|
11 |
BED to BAM |
converter |
|
17 |
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 |
bigwigCompare |
normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them |
|
16 |
Bowtie2 |
- map reads against reference genome |
|
21 |
Build custom track |
for UCSC genome browser |
|
2 |
CEAS |
Annotate intervals and scores with genome features |
|
3 |
Change Case |
of selected columns |
|
1 |
CleanSam |
perform SAM/BAM grooming |
|
12 |
ClosestBed |
find the closest, potentially non-overlapping interval |
|
17 |
ClustalW |
multiple sequence alignment program for DNA or proteins |
|
4 |
Cluster |
the intervals of a dataset |
Sequence clustering
Sequence merging
|
5 |
ClusterBed |
cluster overlapping/nearby intervals |
|
16 |
Collapse |
sequences |
|
3 |
Collect Alignment Summary Metrics |
writes a file containing summary alignment metrics |
|
12 |
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 |
Combine Variants |
|
|
3 |
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 both the depth and breadth of coverage |
of features in file B on the features in file A (bedtools coverage) |
|
17 |
Compute quality statistics |
|
|
3 |
Compute quality statistics |
for SOLiD data |
|
1 |
Compute sequence length |
|
|
6 |
computeGCBias |
Determine the GC bias of your sequenced reads |
|
16 |
computeMatrix |
prepares data for plotting a heatmap or a profile of given regions |
|
17 |
Concatenate |
FASTA alignment by species |
|
2 |
Concatenate |
two datasets into one dataset |
Aggregation
|
5 |
Concatenate datasets |
tail-to-head |
|
1 |
Condense |
consecutive characters |
|
2 |
Convert |
delimiters to TAB |
|
1 |
Convert |
SOLiD output to fastq |
|
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 len file |
|
|
2 |
Convert FASTA to Tabular |
|
|
1 |
Convert from BAM to FastQ |
|
|
13 |
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 SAM |
to interval |
|
2 |
Convert SAM to BAM |
|
|
1 |
Convert tabular to dbnsfp |
|
|
2 |
correctGCBias |
uses the output from computeGCBias to generate GC-corrected BAM/CRAM files |
|
16 |
Count |
occurrences of each record |
|
2 |
Count GFF Features |
|
|
2 |
Coverage |
of a set of intervals on second set of intervals |
Comparison
Filtering
|
5 |
Create single interval |
as a new dataset |
|
1 |
Cuffcompare |
compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments |
|
9 |
Cuffdiff |
find significant changes in transcript expression, splicing, and promoter use |
|
10 |
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 |
Cut |
columns from a table |
|
2 |
Cutadapt |
Remove adapter sequences from Fastq/Fasta |
|
16 |
Depth of Coverage |
on BAM files |
|
3 |
Downsample SAM/BAM |
Downsample a file to retain a subset of the reads |
|
12 |
Draw quality score boxplot |
|
|
5 |
Draw quality score boxplot |
for SOLiD data |
|
1 |
EstimateLibraryComplexity |
assess sequence library complexity from read sequences |
|
12 |
Eval Variants |
|
|
3 |
ExpandBed |
replicate lines based on lists of values in columns |
|
16 |
Extract features |
from GFF data |
|
1 |
Extract Genomic DNA |
using coordinates from assembled/unassembled genomes |
|
8 |
Fasta to Fastq |
converter |
|
1 |
FASTA Width |
formatter |
|
3 |
FASTA-to-Tabular |
converter |
|
4 |
FASTQ Groomer |
convert between various FASTQ quality formats |
Sequence conversion
|
6 |
FASTQ joiner |
on paired end reads |
Aggregation
|
8 |
FASTQ to FASTA |
converter |
Conversion
|
6 |
fastq_screen |
Screen for contamination |
|
1 |
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 |
Fetch closest non-overlapping feature |
for every interval |
Filtering
|
4 |
Filter |
BAM datasets on a variety of attributes |
|
7 |
Filter |
data on any column using simple expressions |
Formatting
|
1 |
Filter Combined Transcripts |
using tracking file |
|
1 |
Filter FASTQ |
reads by quality score and length |
Filtering
|
6 |
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 pileup |
on coverage and SNPs |
|
2 |
Filter SAM |
on bitwise flag values |
|
2 |
Filter sequences by length |
|
Filtering
|
7 |
FilterSamReads |
include or exclude aligned and unaligned reads and read lists |
|
12 |
FIMO |
- Find Individual Motif Occurrences |
|
11 |
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 |
|
12 |
FlankBed |
create new intervals from the flanks of existing intervals |
|
17 |
Gene BED To Exon/Intron/Codon BED |
expander |
|
1 |
Gene Body Coverage (BAM) |
Read coverage over gene body. |
|
9 |
Genome Coverage |
compute the coverage over an entire genome |
|
17 |
Get flanks |
returns flanking region/s for every gene |
Sequence analysis
|
5 |
GetFastaBed |
use intervals to extract sequences from a FASTA file |
|
16 |
GFF-to-BED |
converter |
Conversion
|
1 |
Group |
data by a column and perform aggregate operation on other columns. |
|
5 |
GroupByBed |
group by common cols and summarize other cols |
|
16 |
Haplotype Caller |
Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region |
|
2 |
HISAT2 |
A fast and sensitive alignment program |
|
17 |
Histogram |
of a numeric column |
|
2 |
homer_annotatePeaks |
|
|
1 |
homer_bed2pos |
|
|
1 |
homer_findPeaks |
Homer's peakcaller. Requires tag directories (see makeTagDirectory) |
|
1 |
homer_makeTagDirectory |
Simple wrapper for makeTagDirectory. Used by findPeaks |
|
1 |
homer_pos2bed |
|
|
1 |
htseq-count |
- Count aligned reads in a BAM file that overlap features in a GFF file |
|
9 |
Indel Realigner |
- perform local realignment |
|
3 |
Infer Experiment |
speculates how RNA-seq were configured |
|
9 |
Inner Distance |
calculate the inner distance (or insert size) between two paired RNA reads |
|
9 |
Intersect |
the intervals of two datasets |
Filtering
|
5 |
Intersect intervals |
find overlapping intervals in various ways |
|
17 |
JaccardBed |
calculate the distribution of relative distances between two files |
|
16 |
Join |
the intervals of two datasets side-by-side |
Aggregation
|
5 |
Join two Datasets |
side by side on a specified field |
|
4 |
Line/Word/Character count |
of a dataset |
|
1 |
LinksBed |
create a HTML page of links to UCSC locations |
|
16 |
MACS14 |
Model-based Analysis of ChIP-Seq (1.4.2) |
|
3 |
MACS2 |
Model-based Analysis of ChIP-Seq |
|
2 |
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
|
10 |
MACS2 bdgpeakcall |
Call peaks from bedGraph output |
Regulatory element prediction
|
8 |
MACS2 callpeak |
Call peaks from alignment results |
Regulatory element prediction
|
12 |
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 |
MakeTSSdist |
Get peak distribution around TSS |
|
2 |
MakeWindowsBed |
make interval windows across a genome |
|
17 |
Manipulate FASTQ |
reads on various attributes |
Sequence conversion
|
5 |
Map with Bowtie for Illumina |
|
|
7 |
Map with BWA |
- map short reads (< 100 bp) against reference genome |
|
11 |
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 |
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 |
MeanQualityByCycle |
chart distribution of base qualities |
|
12 |
MEME |
- Multiple Em for Motif Elicitation |
|
1 |
MEME |
- Multiple Em for Motif Elicitation |
|
10 |
Merge |
the overlapping intervals of a dataset |
Sequence merging
|
4 |
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 |
|
12 |
MergeBED |
combine overlapping/nearby intervals into a single interval |
|
16 |
MergeSamFiles |
merges multiple SAM/BAM datasets into one |
|
12 |
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 |
|
16 |
Multiple Intersect |
identifies common intervals among multiple interval files |
|
19 |
NormalizeFasta |
normalize fasta datasets |
|
12 |
NucBed |
profile the nucleotide content of intervals in a FASTA file |
|
17 |
OverlapBed |
computes the amount of overlap from two intervals |
|
16 |
Paste |
two files side by side |
|
1 |
Pileup-to-Interval |
condenses pileup format into ranges of bases |
|
4 |
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 |
|
17 |
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 |
Preprocess files for SARTools |
generate design/target file and archive for SARTools inputs |
|
5 |
Print Reads |
on BAM files |
|
3 |
QualityScoreDistribution |
chart quality score distribution |
|
12 |
RandomBed |
generate random intervals in a genome |
|
17 |
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 |
Reduce Reads |
in BAM files |
|
3 |
ReldistBed |
calculate the distribution of relative distances |
|
16 |
Remove beginning |
of a file |
|
1 |
ReorderSam |
reorder reads to match ordering in reference sequences |
|
15 |
ReplaceSamHeader |
replace header in a SAM/BAM dataset |
|
15 |
Reverse-Complement |
|
|
5 |
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 STAR |
Gapped-read mapper for RNA-seq data |
Mapping assembly
|
13 |
RNA/DNA |
converter |
|
5 |
RNAseqDataAnnotation |
tool for RNAseq data : gene length normalisation and genes annotation |
|
1 |
sam-stats |
- Compute statistics from SAM or BAM files |
|
2 |
SAM-to-BAM |
convert SAM to BAM |
|
11 |
SamToFastq |
extract reads and qualities from SAM/BAM dataset and convert to fastq |
|
17 |
Samtools flagstat |
tabulate descriptive stats for BAM datset |
|
8 |
samtools mpileup |
multi-way pileup of variants |
|
9 |
SARTools DESeq2 |
Compare two or more biological conditions in a RNA-Seq framework with DESeq2 |
|
6 |
Secure Hash / Message Digest |
on a dataset |
|
2 |
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 Variants |
from VCF files |
|
3 |
seqtk_comp |
get the nucleotide composition of FASTA/Q |
|
6 |
seqtk_cutN |
cut sequence at long N |
|
6 |
seqtk_dropse |
drop unpaired from interleaved Paired End FASTA/Q |
|
6 |
seqtk_fqchk |
fastq QC (base/quality summary) |
|
6 |
seqtk_hety |
regional heterozygosity |
|
6 |
seqtk_listhet |
extract the position of each het |
|
6 |
seqtk_mergefa |
merge two FASTA/Q files |
|
6 |
seqtk_mergepe |
interleave two unpaired FASTA/Q files for a paired-end file |
|
6 |
seqtk_mutfa |
point mutate FASTA at specified positions |
|
6 |
seqtk_randbase |
choose a random base from hets |
|
6 |
seqtk_sample |
random subsample of fasta or fastq sequences |
|
6 |
seqtk_seq |
common transformation of FASTA/Q |
|
6 |
seqtk_subseq |
extract subsequences from FASTA/Q files |
|
6 |
seqtk_trimfq |
trim FASTQ using the Phred algorithm |
|
6 |
ShuffleBed |
randomly redistrubute intervals in a genome |
|
17 |
Sickle |
windowed adaptive trimming of FASTQ data |
|
5 |
Slice |
BAM by genomic regions |
|
5 |
SlopBed |
adjust the size of intervals |
|
18 |
SnpEff eff: |
annotate variants |
|
14 |
SnpSift Annotate |
SNPs from dbSnp |
|
7 |
SnpSift CaseControl |
Count samples are in 'case' and 'control' groups. |
|
7 |
SnpSift Filter |
Filter variants using arbitrary expressions |
|
7 |
SnpSift Intervals |
Filter variants using intervals |
|
7 |
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 |
data in ascending or descending order |
|
2 |
SortBED |
order the intervals |
|
16 |
SortSam |
sort SAM/BAM dataset |
|
12 |
SpacingBed |
reports the distances between features |
|
12 |
Split file |
according to the values of a column |
|
1 |
SPP |
SPP cross-correlation analysis package |
|
1 |
Subtract |
the intervals of two datasets |
Filtering
|
5 |
Subtract Whole Dataset |
from another dataset |
|
3 |
SubtractBed |
remove intervals based on overlaps |
|
16 |
Tabular-to-FASTA |
converts tabular file to FASTA format |
|
3 |
TagBed |
tag BAM alignments based on overlaps with interval files |
|
16 |
TopHat |
Gapped-read mapper for RNA-seq data |
|
10 |
TopHat for Illumina |
Find splice junctions using RNA-seq data |
|
3 |
Trim |
leading or trailing characters |
|
1 |
Trim sequences |
|
|
5 |
Unified Genotyper |
SNP and indel caller |
|
3 |
Union of two datasets |
based on common field |
|
1 |
Upload File |
from your computer |
|
2 |
Validate Variants |
|
|
2 |
ValidateSamFile |
assess validity of SAM/BAM dataset |
|
12 |
Variant Annotator |
|
|
3 |
Variant Filtration |
on VCF files |
|
3 |
Variant Recalibrator |
|
|
3 |
Wiggle to Interval |
|
|
2 |
WigMaker |
for BED files |
|
1 |
WindowBed |
find overlapping intervals within a window around an interval |
|
16 |
Zip |
and name files |
|
2 |