Examples : samtools, bed, topic:conversion

352 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset Editing 2
AddCommentsToBam add comments to BAM dataset 14
AddOrReplaceReadGroups add or replaces read group information 14
Advanced Cut columns from a table (cut) 8
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
amrfinder identifies AMR genes using either protein annotations or nucleotide sequence. 1
BamLeftAlign indels in BAM datasets 13
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 2
BedCov calculate read depth for a set of genomic intervals 5
BedToIntervalList convert coordinate data into picard interval list format 14
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
Bowtie2 - map reads against reference genome 19
Call and phase heterozygous SNPs 4
Call variants with LoFreq 6
CalMD recalculate MD/NM tags 5
Canu assembler Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore 4
Change Case of selected columns 2
CleanSam perform SAM/BAM grooming 14
CML to InChI 3
CML to mol2 3
CML to SDF 3
CML to SMILES 3
Collapse Collection into single dataset in order of the collection 5
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 14
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 14
CollectGcBiasMetrics charts the GC bias metrics 14
CollectHsMetrics compute metrics about datasets generated through hybrid-selection (e.g. exome) 3
CollectInsertSizeMetrics plots distribution of insert sizes 14
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 14
Column Join on Collections 5
Compare two Datasets to find common or distinct rows Filtering 1
Compute sequence length 6
Concatenate datasets tail-to-head Aggregation 1
Concatenate datasets tail-to-head (cat) 10
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 2
Convert FASTA to Bowtie color space Index 2
Convert FASTA to fai file 1
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert genome coordinates between assemblies and genomes 2
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
Convert XMFA to gapped GFF3 4
Count occurrences of each record 2
Create assemblies with Unicycler Genome assembly 8
Create single interval as a new dataset 1
Create text file with recurring lines 8
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 8
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cut columns from a table Filtering 2
Cutadapt Remove adapter sequences from Fastq/Fasta Sequence editing 20
Data Fetch Query and retrieval 1
Datamash (operations on tabular data) 3
DAVID functional annotation for a list of genes 1
Delta-Filter Filters alignment (delta) file from nucmer Read mapping Sequence alignment 5
Diamond alignment tool for short sequences against a protein database Sequence alignment analysis 8
Diamond makedb Build database from a FASTA file Sequence alignment analysis 7
Diamond view generate formatted output from DAA files Sequence alignment analysis 5
DNAdiff Evaluate similarities/differences between two sequences Read mapping Sequence alignment 5
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
dRep compare compare a list of genomes 2
dRep dereplicate De-replicate a list of genomes 2
ectyper ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. 1
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
Extract features from GFF data 1
Extract MAF blocks given a set of genomic intervals 3
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
FASTA-to-Tabular converter 3
FASTQ interlacer on paired end reads Aggregation 6
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
FastqToSam convert Fastq data into unaligned BAM 18
FASTTREE build maximum-likelihood phylogenetic trees Phylogenetic analysis Phylogenetic inference (from molecular sequences) 4
Filter data on any column using simple expressions Formatting 2
Filter by quality 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 2
Filter MAF by specified attributes 1
Filter MAF blocks by Species 1
Filter MAF blocks by Size 1
Filter SPAdes repeats Remove short and repeat contigs/scaffolds 1
FilterSamReads include or exclude aligned and unaligned reads and read lists 14
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 14
Flagstat tabulate descriptive stats for BAM datset 8
Flye assembly of long and error-prone reads Genome assembly 7
FreeBayes bayesian genetic variant detector 13
FROGS Abundance normalisation Normalise OTUs abundance. Standardisation and normalisation 4
FROGS Affiliation Filters Filters OTUs on several affiliation criteria. 2
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 4
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 ITSx Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. Sequence trimming 4
FROGS OTU Filters Filters OTUs on several criteria. 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 4
FROGS TSV_to_BIOM Converts a TSV file in a BIOM file. Formatting 4
FROGSSTAT DESeq2 Preprocess import a Phyloseq object and prepare it for DESeq2 differential abundance analysis 2
FROGSSTAT Phyloseq Alpha Diversity with richness plot Taxonomic classification 4
FROGSSTAT Phyloseq Beta Diversity distance matrix Taxonomic classification 4
FROGSSTAT Phyloseq Composition Visualisation with bar plot and composition plot Taxonomic classification 4
FROGSSTAT Phyloseq Import Data from 3 files: biomfile, samplefile, treefile Taxonomic classification 4
FROGSSTAT Phyloseq Multivariate Analysis Of Variance perform Multivariate Analysis of Variance (MANOVA) Taxonomic classification 4
FROGSSTAT Phyloseq Sample Clustering of samples using different linkage methods Taxonomic classification 4
FROGSSTAT Phyloseq Structure Visualisation with heatmap plot and ordination plot Taxonomic classification 4
FROGSTAT Deseq2 Visualisation to extract and visualise differentially abundant OTUs 2
g:Profiler tools for functional profiling of gene lists 1
GATK 3 tool collection Version 3.5-0 1
GeDI Map shotgun metagenomes on reference genomes to estimate microbial ecosystem 1
Genbank to GFF3 converter 2
Gene BED To Exon/Intron/Codon BED expander 1
GFF-to-BED converter Conversion 2
Group data by a column and perform aggregate operation on other columns. 4
heatmap2 4
HISAT2 A fast and sensitive alignment program 18
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes. 2
IdxStats reports stats of the BAM index file 8
InChI to CML 3
InChI to MOL 3
InChI to MOL2 3
InChI to SDF 3
InChI to SMILES 3
Join two files 11
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 4
LD linkage disequilibrium and tag SNPs 1
Line/Word/Character count of a dataset 1
MAF Coverage Stats Alignment coverage information 3
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
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 13
Map with minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences Sequence alignment 18
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 15
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 14
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
MeanQualityByCycle chart distribution of base qualities 14
Merge Columns together 4
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 14
MergeSamFiles merges multiple SAM/BAM datasets into one 14
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 6
metaQuantome: database download the GO, EC, and NCBI databases 6
metaQuantome: expand a set of functional or taxonomy annotations 6
metaQuantome: filter for quality, redundancy, and sample coverage 6
metaQuantome: stat differential analysis of functional expression and taxonomic abundance 6
metaQuantome: visualize taxonomic analysis, functional analysis, and function-taxonomy analysis results 6
miniasm Ultrafast de novo assembly for long noisy reads 7
MOL to CML 3
MOL to MOL2 3
MOL to SMILES 3
MOL2 to CML 3
MOL2 to InChI 3
MOL2 to MOL 3
MOL2 to SDF 3
MOL2 to SMILES 3
Multi-Join (combine multiple files) 9
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 17
Mummer Align two or more sequences Read mapping Sequence alignment 5
Mummerplot Generate 2-D dotplot of aligned sequences Read mapping Sequence alignment 5
MUSCLE multiple aligner Multiple sequence alignment 3
NanoFilt Filtering and trimming of long read sequencing data 1
NanoPlot Plotting suite for Oxford Nanopore sequencing data and alignments 5
NCBI Accession Download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 2
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 13
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 12
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 13
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 18
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NormalizeFasta normalize fasta datasets 14
Nucmer Align two or more sequences Read mapping Sequence alignment 5
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
ParSNP Efficient microbial core genome alignment and SNP detection Phylogenetic inference Sequence comparison 1
Paste two files side by side 1
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 4
Porechop adapter trimmer for Oxford Nanopore reads 3
Preprocess files for SARTools generate design/target file and archive for SARTools inputs 4
Preprocess GeDI UnArchive file 1
PRINSEQ to process quality of sequences 5
printenv 1
prodigal Find genes 2
progressiveMauve constructs multiple genome alignments 4
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 11
QualityScoreDistribution chart quality score distribution 14
Quast Genome assembly Quality 11
Reheader copy SAM/BAM header between datasets 4
Remove beginning of a file 1
ReorderSam reorder reads to match ordering in reference sequences 17
Replace parts of text 11
Replace Text in entire line 11
Replace Text in a specific column 11
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Reverse Complement a MAF file 1
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
RevertSam revert SAM/BAM datasets to a previous state 14
Roary the pangenome pipeline - Quickly generate a core gene alignment from gff3 files 8
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 18
Samtools coverage computes the depth at each position or region 1
Samtools depth compute the depth at each position or region 3
Samtools fastx extract FASTA or FASTQ from alignment files 2
Samtools fixmate fill mate coordinates, ISIZE and mate related flags 2
Samtools markdup marks duplicate alignments 5
Samtools merge merge multiple sorted alignment files 3
samtools mpileup multi-way pileup of variants 11
Samtools sort order of storing aligned sequences 7
Samtools stats generate statistics for BAM dataset 6
Samtools view - reformat, filter, or subsample SAM, BAM or CRAM 9
SARTools DESeq2 Compare two or more biological conditions in a RNA-Seq framework with DESeq2 4
SARTools edgeR Compare two or more biological conditions in a RNA-Seq framework with edgeR 4
Scatterplot with ggplot2 6
SDF to CML 3
SDF to InChI 3
SDF to mol2 3
SDF to SMILES 3
Search in textfiles (grep) 10
Secure Hash / Message Digest on a dataset 2
Select lines that match an expression Filtering 3
Select first lines from a dataset Filtering 3
Select first lines from a dataset (head) 8
Select last lines from a dataset 2
Select last lines from a dataset (tail) 8
Select random lines from a file 2
Send to cloud 1
SeqSero2 v1.1.1 Salmonella serotype prediction 1
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
SFF converter 1
Shasta De novo assembly of long read sequencing data 1
Shovill Faster SPAdes assembly of Illumina reads 7
Show-Coords Parse delta file and report coordinates and other information Read mapping Sequence alignment 5
Sickle windowed adaptive trimming of FASTQ data 4
SMILES to CML 3
SMILES to InChI 3
SMILES to MOL 3
SMILES to MOL2 3
SMILES to SDF 3
SMILES to SMILES 3
snippy Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 11
snippy-clean_full_aln Replace any non-standard sequence characters in snippy 'core.full.aln' file. 4
snippy-core Combine multiple Snippy outputs into a core SNP alignment 11
SnpEff build: database from Genbank or GFF record 12
SnpEff chromosome-info: list chromosome names/lengths 7
SnpEff databases: list available databases 12
SnpEff download: download a pre-built database 15
SnpEff eff: annotate variants 13
SnpSift 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 6
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 8
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 data in ascending or descending order 3
Sort data in ascending or descending order 10
Sort a row according to their columns 11
SortSam sort SAM/BAM dataset 14
SPAdes genome assembler for regular and single-cell projects Genome assembly 13
Split BAM dataset on readgroups 4
Split MAF blocks by Species 1
staramr Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes. 9
Stitch Gene blocks given a set of coding exon intervals 4
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 14
StringTie merge transcripts 8
Summary Statistics for any numerical column 3
Tabular-to-FASTA converts tabular file to FASTA format 2
tac reverse a file (reverse cat) 8
Text reformatting with awk 12
Text transformation with sed 10
Trim leading or trailing characters 2
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 15
Unfold columns from a table 10
Unique occurrences of each record 1
Unique occurrences of each record 8
Unique lines assuming sorted input file 10
Upload File from your computer Query and retrieval 3
Upload local file to current History 1
ValidateSamFile assess validity of SAM/BAM dataset 14
VCF to MAF Custom Track for display at UCSC 2
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
Wiggle-to-Interval converter 2