Examples : samtools, bed, topic:conversion

398 tool(s) found

Tool Description Topics Available version(s)
ABySS de novo sequence assembler 9
Add column to an existing dataset Editing 2
AddCommentsToBam add comments to BAM dataset 14
AddOrReplaceReadGroups add or replaces read group information 14
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 12
alignmentsieve Filter BAM/CRAM files according to specified parameters 7
alimask append modelmask line to a multiple sequence alignments 7
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
BAM-to-SAM convert BAM to SAM 5
bamCompare normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them 16
bamCoverage generates a coverage bigWig file from a given BAM or CRAM file 18
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
Bar chart for multiple columns 2
Barcode Splitter 4
bcf_uncompressed-to-bcf converter 1
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BedCov calculate read depth for a set of genomic intervals 5
BedToIntervalList convert coordinate data into picard interval list format 14
bedtools AnnotateBed annotate coverage of features from multiple files 21
bedtools BAM to BED converter 23
bedtools BED to BAM converter 21
bedtools BED to IGV create batch script for taking IGV screenshots 16
bedtools BED12 to BED6 converter 20
bedtools BEDPE to BAM converter 21
bedtools ClosestBed find the closest, potentially non-overlapping interval 21
bedtools ClusterBed cluster overlapping/nearby intervals 20
bedtools ComplementBed Extract intervals not represented by an interval file 21
bedtools ExpandBed replicate lines based on lists of values in columns 20
bedtools FisherBed calculate Fisher statistic between two feature files 20
bedtools FlankBed create new intervals from the flanks of existing intervals 21
bedtools Genome Coverage compute the coverage over an entire genome 20
bedtools GroupByBed group by common cols and summarize other cols 20
bedtools JaccardBed calculate the distribution of relative distances between two files 20
bedtools LinksBed create a HTML page of links to UCSC locations 20
bedtools MakeWindowsBed make interval windows across a genome 21
bedtools MaskFastaBed use intervals to mask sequences from a FASTA file 20
bedtools Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 20
bedtools MergeBED combine overlapping/nearby intervals into a single interval 20
bedtools MultiCovBed counts coverage from multiple BAMs at specific intervals 20
bedtools Multiple Intersect identifies common intervals among multiple interval files 23
bedtools OverlapBed computes the amount of overlap from two intervals 20
bedtools RandomBed generate random intervals in a genome 21
bedtools ReldistBed calculate the distribution of relative distances 20
bedtools ShuffleBed randomly redistrubute intervals in a genome 21
bedtools SlopBed adjust the size of intervals 22
bedtools SortBED order the intervals 20
bedtools SpacingBed reports the distances between features 17
bedtools SubtractBed remove intervals based on overlaps 20
bedtools TagBed tag BAM alignments based on overlaps with interval files 20
bedtools WindowBed find overlapping intervals within a window around an interval 20
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 18
BlastAlign Align the nucleic acid sequences using BLASTN 1
Bowtie2 - map reads against reference genome 21
Boxplot of quality statistics 2
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 12
Busco assess genome assembly and annotation completeness 15
CDS_search ORF and CDS search 2
Change Case of selected columns 2
Choose Patterns of Interest in a Multiple Condition Design Choose patterns of interest in a multiple condition design 1
CleanSam perform SAM/BAM grooming 14
Clip adapter sequences 6
CML to InChI 2
CML to mol2 2
CML to SDF 2
cml-to-smi converter 2
codeML Detects positive selection (paml package) 3
Collapse sequences 3
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
CollectInsertSizeMetrics plots distribution of insert sizes 14
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 15
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 14
Compare two Datasets to find common or distinct rows Filtering 1
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 21
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 10
Compute quality statistics 3
computeGCBias Determine the GC bias of your sequenced reads 17
computeMatrix prepares data for plotting a heatmap or a profile of given regions 18
computeMatrixOperations Modify or combine the output of computeMatrix in a variety of ways. 11
Concatenate two BED files Aggregation 6
Concatenate datasets tail-to-head Aggregation 1
ConcatPhyl Concatenation and phylogeny 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 FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 2
Convert FASTA to Bowtie color space Index 2
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
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Count occurrences of each record 2
Create single interval as a new dataset 1
csv-to-tabular converter 1
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 8
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 11
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
Cuffnorm Create normalized expression levels 7
Cuffquant Precompute gene expression levels 4
Cut columns from a table Filtering 2
Data Fetch Query and retrieval 1
dbnsfp.tabular-to-snpsiftdbnsfp converter 3
Describe samples and replicates 11
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 22
Diamond alignment tool for short sequences against a protein database Sequence alignment analysis 9
Diamond makedb Build database from a FASTA file Sequence alignment analysis 8
Diamond view generate formatted output from DAA files Sequence alignment analysis 6
Differential expression analysis using a Trinity assembly 11
Download and Extract Reads in BAM format from NCBI SRA Data retrieval Formatting 24
Download and Extract Reads in FASTQ format from NCBI SRA Data retrieval Formatting 20
Download and Generate Pileup Format from NCBI SRA 9
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
Draw nucleotides distribution chart 4
Draw quality score boxplot 4
edgeR Perform differential expression of count data Differential gene expression profiling RNA-seq read count analysis 10
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
estimateReadFiltering estimates the number of reads that would be filtered given certain criteria 6
Extract and cluster differentially expressed transcripts from a Trinity assembly 12
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
faSplit Split a FASTA file 3
FASTA Width formatter 3
fasta-to-fai converter 1
Faster Download and Extract Reads in FASTQ format from NCBI SRA Data retrieval Formatting 15
fastp - fast all-in-one preprocessing for FASTQ files 8
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 5
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 6
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
FastqToSam convert Fastq data into unaligned BAM 19
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 25
Filter data on any column using simple expressions Formatting 2
Filter assemblies Filter the outputs of Velvet or Trinity assemblies 1
Filter by quality Filtering 6
Filter GFF data by attribute using simple expressions 2
Filter GFF data by feature count using simple expressions 1
Filter GTF data by attribute values_list 2
Filter low expression transcripts from a Trinity assembly 11
Filter SAM on bitwise flag values 1
Filter sequences by ID from a tabular file 5
Filter sequences by length Filtering 6
Filter with SortMeRNA of ribosomal RNAs in metatranscriptomic data 6
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
GATK 3 tool collection Version 3.5-0 1
GATK4 Mutect2 - Call somatic SNVs and indels via local assembly of haplotypes 8
Gene BED To Exon/Intron/Codon BED expander 1
Gene level DE test across multiple conditions Runs EBSeq to find DE genes across multiple (more than two) conditions 1
Gene level DE test across two conditions Runs EBSeq to find DE genes across two conditions 1
Generate gene to transcript map for Trinity assembly 10
Generate SuperTranscripts from a Trinity assembly 6
Get All Possible Patterns in a Multiple Condition Design Get all possible patterns in a multiple condition design 1
Get Ig vector from gene-isoform mapping for isoform level DE analysis Get Ig vector from gene-isoform mapping for isoform level DE analysis 1
Get Microbial Data Query and retrieval 1
Get Normalized Expressions Calculate normalization factors and get the normalized expression matrix 1
GetFastaBed use intervals to extract sequences from a FASTA file 20
GFF-to-BED converter Conversion 1
GffCompare compare assembled transcripts to a reference annotation 5
gffread Filters and/or converts GFF3/GTF2 records 7
goseq tests for overrepresented gene categories Gene-set enrichment analysis 12
Group data by a column and perform aggregate operation on other columns. 4
GTF-to-BEDGraph converter Conversion 1
Heatmap Heatmap of the dataMatrix 2
heatmap2 6
HISAT2 A fast and sensitive alignment program 19
hmmalign align sequences to a profile HMM 7
hmmbuild Build a profile HMM from an input multiple alignment 8
hmmconvert convert profile file to a HMMER format 7
hmmemit sample sequence(s) from a profile HMM 7
hmmfetch retrieve profile HMM(s) from a file 7
hmmscan search sequence(s) against a profile database 8
hmmsearch search profile(s) against a sequence database 8
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
IdxStats reports stats of the BAM index file 8
InChI to CML 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
inchi-to-mol converter 2
Intersect the intervals of two datasets Filtering 6
Intersect intervals find overlapping intervals in various ways 22
Isoform level DE test across multiple conditions Runs EBSeq to find DE isoforms across multiple (more than two) conditions 1
Isoform level DE test across two conditions Runs EBSeq to find DE isoforms across two conditions 1
jackhmmer iteratively search a protein sequence against a protein database (PSIBLAST-like) 8
Join the intervals of two datasets side-by-side Aggregation 5
Join two Datasets side by side on a specified field 4
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 6
Kallisto quant - quantify abundances of RNA-Seq transcripts 8
LAST-split finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA). 4
LAST-train finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences. 5
LASTal finds local alignments between query sequences, and reference sequences. 6
LASTdb prepares sequences for subsequent comparison and alignment using lastal. 5
LAV to BED Converts a LAV formatted file to BED format 1
Length Distribution chart 2
Line/Word/Character count of a dataset 1
MACS2 bdgbroadcall Call broad peaks from bedGraph output 9
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph 9
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files 10
MACS2 bdgpeakcall Call peaks from bedGraph output 9
MACS2 callpeak Call peaks from alignment results 12
MACS2 filterdup Remove duplicate reads at the same position 9
MACS2 predictd Predict 'd' or fragment size from alignment results 9
MACS2 randsample Randomly sample number or percentage of total reads 9
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) 9
MAF-convert read MAF-format alignments and write them in another format. 4
Maker genome annotation pipeline 10
Map annotation ids on a Maker annotation 5
Map with Bowtie for Illumina 7
Map with BWA - map short reads (< 100 bp) against reference genome 12
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 14
MapBed apply a function to a column for each overlapping interval 21
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 17
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 16
MeanQualityByCycle chart distribution of base qualities 14
Merge the overlapping intervals of a dataset Sequence merging 5
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
MIRA v4.0 de novo assember Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads 2
MIRA v4.0 mapping Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads 2
MIRA v4.0 mirabait Filter reads using kmer matches 2
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to SDF 2
MOL2 to SMILES 2
mol2-to-mol converter 2
mothur.ref.taxonomy-to-mothur.seq.taxonomy converter 2
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
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 18
MutCount This tool proceeds to count codons, amino acids on each species of a set of species, and then proceeds to permutation tests. 1
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 18
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 18
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 15
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 18
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 16
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 18
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 14
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 15
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 19
nhmmer search a DNA model or alignment against a DNA database (BLASTN-like) 8
nhmmscan search DNA sequence(s) against a DNA profile database 8
NormalizeFasta normalize fasta datasets 14
NucBed profile the nucleotide content of intervals in a FASTA file 21
Oligator Oligator: design PCR primers 1
OrthoFinder finds orthogroups in a set of proteomes 7
Orthogroups_Tool Writes orthogroups found by OrthoFinder in fasta files (with their sequences). 1
Pairwise Find homologous couples by blast with RBH 1
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 12
Paste two files side by side 1
Pear Paired-End read merger 5
phmmer search a protein sequence against a protein database (BLASTP-like) 8
Phyogenetic reconstruction with RAxML - Maximum Likelihood based inference of large phylogenetic trees 6
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 assesing 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
POGs Find orthologous groups 1
Preprocess files for SARTools generate design/target file and archive for SARTools inputs 4
PRINSEQ to process quality of sequences 5
Quality format converter (ASCII-Numeric) 3
QualityScoreDistribution chart quality score distribution 14
Reheader copy SAM/BAM header between datasets 4
Remove beginning of a file 1
Remove sequencing artifacts 5
Rename sequences 5
ReorderSam reorder reads to match ordering in reference sequences 17
RepeatMasker screen DNA sequences for interspersed repeats and low complexity regions Repeat sequence analysis 8
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Reverse-Complement 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
RevertSam revert SAM/BAM datasets to a previous state 14
RmDup remove PCR duplicates 5
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly Sequence alignment 19
RNA/DNA converter 5
RNASeq samples quality check for transcript quantification 11
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 1
Salmon quant Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads 13
SAM-to-BAM convert SAM to BAM 8
sam-to-unsorted.bam converter 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 19
Samtools calmd recalculate MD/NM tags 4
Samtools flagstat tabulate descriptive stats for BAM datset 8
samtools mpileup multi-way pileup of variants 11
Samtools sort order of storing aligned sequences 7
Samtools split BAM dataset on readgroups 5
Samtools stats generate statistics for BAM dataset 7
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
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 Filtering 3
Select first lines from a dataset Filtering 4
Select last lines from a dataset 2
Select random lines from a file 2
SFF converter 1
Sickle windowed adaptive trimming of FASTQ data 4
SignalP 3.0 Find signal peptides in protein sequences 4
Slice BAM by genomic regions 5
smi-to-mol converter 2
smi-to-smi converter 2
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL2 2
SMILES to SDF 2
SnpEff databases: list available databases 13
SnpEff download: download a pre-built database 13
SnpEff eff: annotate variants 11
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift dbNSFP Add annotations from dbNSFP or similar annotation DBs 4
SnpSift Extract Fields from a VCF file into a tabular file 7
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 9
SnpSift rmInfo remove INFO field annotations 8
SnpSift Variant Type Annotate with variant type 8
SnpSift vcfCheck basic checks for VCF specification compliance 8
Sort data in ascending or descending order Sorting 3
SortSam sort SAM/BAM dataset 14
SPAdes genome assembler for genomes of regular and single-cell projects Genome assembly 16
Stacks: assemble read pairs by locus run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers 6
Stacks: clone filter Identify PCR clones 2
Stacks: cstacks build a catalogue of loci 5
Stacks: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 5
Stacks: genotypes analyse haplotypes or genotypes in a genetic cross ('genotypes' program) 5
Stacks: populations analyze a population of individual samples ('populations' program) 5
Stacks: process radtags the Stacks demultiplexing script 5
Stacks: pstacks find stacks from short reads mapped to a reference genome 5
Stacks: reference map the Stacks pipeline with a reference genome (ref_map.pl) 5
Stacks: rxstacks make corrections to genotype and haplotype calls 5
Stacks: sstacks match stacks to a catalog 4
Stacks: statistics on stacks found for multiple samples 2
Stacks: ustacks align short reads into stacks 5
StringTie transcript assembly and quantification 17
StringTie merge transcripts 11
Structure using multi-locus genotype data to investigate population structure 2
structureHarvester for parsing STRUCTURE outputs and for performing the Evanno method 1
Subtract the intervals of two datasets Filtering 6
Summary Statistics for any numerical column 3
tabular-to-csv converter 1
tar-to-directory converter 2
TMHMM 2.0 Find transmembrane domains in protein sequences 5
TopHat Gapped-read mapper for RNA-seq data 9
Tophat for Illumina Find splice junctions using RNA-seq data 2
TransDecoder finds coding regions within transcripts 7
Transpose rows/columns in a tabular file 5
Trim leading or trailing characters 2
Trim sequences 5
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 15
Trinity de novo assembly of RNA-Seq data 14
Trinity Statistics Obtain basic stats for the number of genes and isoforms and contiguity of the assembly 1
Trinotate functional transcript annotation 4
Upload File from your computer Query and retrieval 3
ValidateSamFile assess validity of SAM/BAM dataset 15
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2