Examples : samtools, bed, topic:conversion

228 tool(s) found

Tool Description Topics Available version(s)
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