Add column |
to an existing dataset |
|
3 |
AddCommentsToBam |
add comments to BAM dataset |
|
12 |
AddOrReplaceReadGroups |
add or replaces read group information |
|
12 |
BamLeftAlign |
indels in BAM datasets |
|
8 |
bcftools mpileup |
Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files |
|
6 |
BED-to-bigBed |
converter |
Conversion
|
2 |
BED-to-GFF |
converter |
Conversion
|
1 |
BedCov |
calculate read depth for a set of genomic intervals |
|
4 |
BedToIntervalList |
convert coordinate data into picard interval list format |
|
12 |
Bowtie2 |
- map reads against reference genome |
|
21 |
Call and phase |
heterozygous SNPs |
|
5 |
CalMD |
recalculate MD/NM tags |
|
5 |
Change Case |
of selected columns |
|
1 |
CleanSam |
perform SAM/BAM grooming |
|
12 |
CML to InChI |
|
|
2 |
CML to mol2 |
|
|
2 |
CML to SDF |
|
|
2 |
CML to SMILES |
|
|
2 |
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 |
CollectHsMetrics |
compute metrics about datasets generated through hybrid-selection (e.g. exome) |
|
3 |
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 |
Compare two Datasets |
to find common or distinct rows |
|
1 |
Compute sequence length |
|
|
6 |
Concatenate datasets |
tail-to-head |
|
1 |
Convert |
delimiters to TAB |
|
1 |
Convert BCF to uncompressed BCF |
|
|
1 |
Convert BED to Feature Location Index |
|
|
1 |
Convert BED to GFF |
|
|
2 |
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 |
|
|
2 |
Convert FASTA to Tabular |
|
|
1 |
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 without sorting |
|
|
1 |
Convert tabular to CSV |
|
|
1 |
Convert tabular to dbnsfp |
|
|
2 |
Convert tar to directory |
|
|
2 |
Convert uncompressed BCF to BCF |
|
|
1 |
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 |
|
9 |
Cufflinks |
transcript assembly and FPKM (RPKM) estimates for RNA-Seq data |
|
8 |
Cut |
columns from a table |
|
2 |
Cutadapt |
Remove adapter sequences from Fastq/Fasta |
|
16 |
Data Fetch |
|
|
1 |
Downsample SAM/BAM |
Downsample a file to retain a subset of the reads |
|
12 |
EstimateLibraryComplexity |
assess sequence library complexity from read sequences |
|
12 |
Extract features |
from GFF data |
|
1 |
FASTA-to-Tabular |
converter |
|
4 |
FASTQ interlacer |
on paired end reads |
Aggregation
|
6 |
FastQC |
Read Quality reports |
Sequence composition calculation
Sequencing quality control
Statistical calculation
|
19 |
FastqToSam |
convert Fastq data into unaligned BAM |
|
15 |
Filter |
data on any column using simple expressions |
Formatting
|
1 |
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 |
FilterSamReads |
include or exclude aligned and unaligned reads and read lists |
|
12 |
FixMateInformation |
ensure that all mate-pair information is in sync between each read and it's mate pair |
|
12 |
FreeBayes |
bayesian genetic variant detector |
|
8 |
FROGS Abundance normalisation |
Normalize OTUs abundance. |
Standardisation and normalisation
|
4 |
FROGS Affiliation OTU |
Taxonomic affiliation of each OTU's seed by RDPtools and BLAST |
Taxonomic classification
|
4 |
FROGS Affiliation postprocess |
Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics |
Taxonomic classification
|
2 |
FROGS Affiliations stat |
Process some metrics on taxonomies. |
Taxonomic classification
|
4 |
FROGS BIOM to std BIOM |
Converts a FROGS BIOM in fully compatible BIOM. |
Formatting
|
4 |
FROGS BIOM to TSV |
Converts a BIOM file in TSV file. |
Formatting
|
4 |
FROGS Clustering swarm |
Single-linkage clustering on sequences |
Taxonomic classification
|
4 |
FROGS Clusters stat |
Process some metrics on clusters. |
Clustering
|
4 |
FROGS Demultiplex reads |
Attribute reads to samples in function of inner barcode. |
Classification
|
4 |
FROGS Filters |
Filters OTUs on several criteria. |
Taxonomic classification
|
4 |
FROGS ITSx |
Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. |
Sequence trimming
|
2 |
FROGS Pre-process |
merging, denoising and dereplication. |
Filtering
|
4 |
FROGS Remove chimera |
Remove PCR chimera in each sample. |
Editing
|
4 |
FROGS Tree |
Reconstruction of phylogenetic tree |
Taxonomic classification
|
2 |
FROGS TSV_to_BIOM |
Converts a TSV file in a BIOM file. |
Formatting
|
3 |
FROGSSTAT Phyloseq Alpha Diversity |
with richness plot |
Taxonomic classification
|
2 |
FROGSSTAT Phyloseq Beta Diversity |
distance matrix |
Taxonomic classification
|
2 |
FROGSSTAT Phyloseq Composition Visualisation |
with bar plot and composition plot |
Taxonomic classification
|
2 |
FROGSSTAT Phyloseq Import Data |
from 3 files: biomfile, samplefile, treefile |
Taxonomic classification
|
2 |
FROGSSTAT Phyloseq Multivariate Analysis Of Variance |
perform Multivariate Analysis of Variance (MANOVA) |
Taxonomic classification
|
2 |
FROGSSTAT Phyloseq Sample Clustering |
of samples using different linkage methods |
Taxonomic classification
|
2 |
FROGSSTAT Phyloseq Structure Visualisation |
with heatmap plot and ordination plot |
Taxonomic classification
|
2 |
GATK 3 |
tool collection Version 3.5-0 |
|
1 |
GeDI |
Map shotgun metagenomes on reference genomes to estimate microbial ecosystem |
|
1 |
GFF-to-BED |
converter |
Conversion
|
1 |
Group |
data by a column and perform aggregate operation on other columns. |
|
5 |
HISAT2 |
A fast and sensitive alignment program |
|
17 |
htseq-count |
- Count aligned reads in a BAM file that overlap features in a GFF file |
|
9 |
InChI to CML |
|
|
2 |
InChI to MOL |
|
|
2 |
InChI to MOL2 |
|
|
2 |
InChI to SDF |
|
|
2 |
InChI to SMILES |
|
|
2 |
Join two Datasets |
side by side on a specified field |
|
4 |
Line/Word/Character count |
of a dataset |
|
1 |
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 |
MarkDuplicates |
examine aligned records in BAM datasets to locate duplicate molecules |
|
13 |
MarkDuplicatesWithMateCigar |
examine aligned records in BAM datasets to locate duplicate molecules |
|
12 |
MeanQualityByCycle |
chart distribution of base qualities |
|
12 |
Merge Columns |
together |
|
2 |
MergeBamAlignment |
merge alignment data with additional info stored in an unmapped BAM dataset |
|
12 |
MergeSamFiles |
merges multiple SAM/BAM datasets into one |
|
12 |
MetaFoldScan |
Scan metagenomes and identify fold hits associated to a target protein structurally characterized |
|
1 |
MetaFoldScan Filtering Tool |
|
|
1 |
metaQuantome: create samples file |
by specifying the experiment's groups and associated column names |
|
4 |
metaQuantome: database |
download the GO, EC, and NCBI databases |
|
4 |
metaQuantome: expand |
a set of functional or taxonomy annotations |
|
5 |
metaQuantome: filter |
for quality, redundancy, and sample coverage |
|
5 |
metaQuantome: stat |
differential analysis of functional expression and taxonomic abundance |
|
5 |
metaQuantome: visualize |
taxonomic analysis, functional analysis, and function-taxonomy analysis results |
|
5 |
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 |
MultiQC |
aggregate results from bioinformatics analyses into a single report |
Statistical calculation
Validation
Visualisation
|
11 |
Muscle |
Multiple sequence alignment |
Multiple sequence alignment
|
3 |
NormalizeFasta |
normalize fasta datasets |
|
12 |
PAQmiR Create miRNA/Precursors reference files |
creates the microRNA reference files used by the miRDeep2 software |
|
1 |
PAQmiR Cut Fasta identifiers |
modifies the sequences headers in fasta file by removing all annotations located after the first space |
|
1 |
PAQmiR MiRDeep2 |
identification of novel and known miRNAs |
|
1 |
PAQmiR MiRDeep2 Mapper |
process and map reads to a reference genome |
|
1 |
PAQmiR MiRDeep2 Quantifier |
fast quantitation of reads mapping to known miRBase precursors |
|
1 |
PAQmiR Postprocess MiRDeep2 |
filter and use the results of miRDeep2 to create new reference datasets for quantification and annotation steps |
|
1 |
PAQmiR Postprocess Quantifier |
filters results to quantify, annotate, and eliminate redundancy in miRNAs |
|
1 |
Paste |
two files side by side |
|
1 |
Picard Collect Sequencing Artifact Metrics |
Collect metrics to quantify single-base sequencing artifacts |
|
3 |
Preprocess files for SARTools |
generate design/target file and archive for SARTools inputs |
|
5 |
Preprocess GeDI |
UnArchive file |
|
1 |
PRINSEQ |
to process quality of sequences |
|
3 |
printenv |
|
|
1 |
prodigal |
Find genes |
|
1 |
Prokka |
Prokaryotic genome annotation |
Coding region prediction
Gene prediction
Genome annotation
|
8 |
QualityScoreDistribution |
chart quality score distribution |
|
12 |
Quast |
Genome assembly Quality |
|
8 |
Reheader |
copy SAM/BAM header between datasets |
|
2 |
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 |
RevertOriginalBaseQualitiesAndAddMateCigar |
revert the original base qualities and add the mate cigar tag |
|
12 |
RevertSam |
revert SAM/BAM datasets to a previous state |
|
12 |
SamToFastq |
extract reads and qualities from SAM/BAM dataset and convert to fastq |
|
17 |
Samtools depth |
compute the depth at each position or region |
|
1 |
Samtools fastx |
extract FASTA or FASTQ from alignment files |
|
2 |
Samtools fixmate |
fill mate coordinates, ISIZE and mate related flags |
|
1 |
Samtools flagstat |
tabulate descriptive stats for BAM datset |
|
8 |
Samtools idxstats |
reports stats of the BAM index file |
|
8 |
Samtools markdup |
marks duplicate alignments |
|
2 |
Samtools merge |
merge multiple sorted alignment files |
|
1 |
samtools mpileup |
multi-way pileup of variants |
|
9 |
Samtools sort |
order of storing aligned sequences |
|
7 |
Samtools stats |
generate statistics for BAM dataset |
|
7 |
Samtools view |
reformat, filter, or subsample |
|
4 |
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 |
|
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 |
SFF converter |
|
|
1 |
Sickle |
windowed adaptive trimming of FASTQ data |
|
5 |
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 build: |
database from Genbank or GFF record |
|
10 |
SnpEff chromosome-info: |
list chromosome names/lengths |
|
4 |
SnpEff databases: |
list available databases |
|
12 |
SnpEff download: |
download a pre-built database |
|
12 |
SnpEff eff: |
annotate variants |
|
14 |
SnpSift Annotate |
SNPs from dbSnp |
|
7 |
SnpSift CaseControl |
Count samples are in 'case' and 'control' groups. |
|
7 |
SnpSift Extract Fields |
from a VCF file into a tabular file |
|
5 |
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 |
SortSam |
sort SAM/BAM dataset |
|
12 |
SPAdes |
genome assembler for regular and single-cell projects |
Genome assembly
|
11 |
Split |
BAM dataset on readgroups |
|
3 |
Summary Statistics |
for any numerical column |
|
3 |
Tabular-to-FASTA |
converts tabular file to FASTA format |
|
3 |
Trim |
leading or trailing characters |
|
1 |
Trimmomatic |
flexible read trimming tool for Illumina NGS data |
Sequence trimming
|
14 |
Upload File |
from your computer |
|
2 |
Upload local file |
to current History |
|
1 |
ValidateSamFile |
assess validity of SAM/BAM dataset |
|
12 |
velvetg |
Velvet sequence assembler for very short reads |
De-novo assembly
Formatting
|
6 |
velveth |
Prepare a dataset for the Velvet velvetg Assembler |
De-novo assembly
Formatting
|
6 |
VelvetOptimiser |
Automatically optimize Velvet assemblies |
|
5 |
Wig/BedGraph-to-bigWig |
converter |
|
2 |
Wiggle to Interval |
|
|
2 |