Examples : samtools, bed, topic:conversion

404 tool(s) found

Tool Description Topics Available version(s)
AddCommentsToBam add comments to BAM dataset 14
AddOrReplaceReadGroups add or replaces read group information 14
Align sequences to a reference using a codon alignment algorithm 6
Annotate a newick tree with HyPhy 6
Annotate DESeq2/DEXSeq output tables Append annotation from GTF to differential expression tool outputs 2
annotatePeaks 4
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 5
ArgosDB BioSample scrape Scrape NCBI Biosample for ArgosDB 1
ArgosDB SRA scrape Scrape NCBI SRA Metadata for ArgosDB 1
backtranseq Back translate a protein sequence 7
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 10
bam-to-bai converter 1
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 10
bamCoverage generates a coverage bigWig file from a given BAM or CRAM file 18
banana Bending and curvature plot in B-DNA 5
BBTools: BBMap short-read aligner 4
bcf_uncompressed-to-bcf converter 1
bcftools annotate Annotate and edit VCF/BCF files 11
bcftools call SNP/indel variant calling from VCF/BCF 12
Beast Bayesian MCMC analysis of molecular sequences. 1
bedgraph-to-bigwig converter 1
BedToIntervalList convert coordinate data into picard interval list format 14
biom2-to-biom1 converter 1
Biosample from SRA Get BioSample associated to SRA metadata 1
biosed Replace or delete sequence sections 5
Bismark Deduplicate Deduplicates reads mapped by Bismark 9
Bismark Mapper Bisulfite reads mapper 15
Bismark Meth. Extractor Reports on methylation status of reads mapped by Bismark 11
Bismark Pretty Report Generates a graphical HTML report page from report outputs of Bismark 9
Bowtie2 - map reads against reference genome 21
btwisted Calculates the twisting in a B-DNA sequence 5
BWA-MEM2 - map medium and long reads (> 100 bp) against reference genome 1
bwameth Fast and accurate aligner of BS-Seq reads. 6
cai CAI codon adaptation index 5
cai custom CAI codon adaptation index using custom codon usage file 5
Calculate sequence complexity total and per read 3
Call variants with LoFreq 7
Change Case of selected columns 2
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 5
checktrans Reports STOP codons and ORF statistics of a protein 5
chips Codon usage statistics 5
cirdna Draws circular maps of DNA constructs 5
CleanSam perform SAM/BAM grooming 14
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 10
cml-to-mol2 converter 1
cml-to-smi converter 2
codcmp Codon usage table comparison 5
coderet Extract CDS, mRNA and translations from feature tables 5
Collapse sequences 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) 4
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
compseq Count composition of dimer/trimer/etc words in a sequence 5
Compute on rows 10
Compute quality statistics 3
computeMatrix prepares data for plotting a heatmap or a profile of given regions 18
Concatenate datasets tail-to-head (cat) 11
Convert BAM to FASTA multiple sequence alignment 5
Convert BED to Feature Location Index 1
Convert BED to GFF 2
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 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 GTF to BED12 1
Convert Kraken data to Galaxy taxonomy representation 3
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
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 5
cram-to-bam converter 2
Create assemblies with Unicycler pipeline for bacterial genomes Genome assembly 10
Create text file with recurring lines 9
csv-to-tabular converter 1
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
cusp Create a codon usage table 5
Cut columns from a table Filtering 2
Cut columns from a table (cut) 9
Cutadapt Remove adapter sequences from FASTQ/FASTA Sequence editing 22
cutseq Removes a specified section from a sequence 5
dada2: plotComplexity Plot sequence complexity profile 6
dan Calculates DNA RNA/DNA melting temperature 5
Data Fetch Query and retrieval 1
Datamash (operations on tabular data) 5
dbnsfp.tabular-to-snpsiftdbnsfp converter 3
degapseq Removes gap characters from sequences 5
Deletion Profile calculates the distributions of deleted nucleotides across reads 6
descseq Alter the name or description of a sequence 5
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 22
diffseq Find differences between nearly identical sequences 5
digest Protein proteolytic enzyme or reagent cleavage digest 5
dotmatcher Displays a thresholded dotplot of two sequences 5
dotpath Non-overlapping wordmatch dotplot of two sequences 5
dottup Displays a wordmatch dotplot of two sequences 5
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
dreg Regular expression search of a nucleotide sequence 6
DropletUtils Utilities for handling droplet-based single-cell RNA-seq data DNA barcoding Parsing 9
edgeR Perform differential expression of count data Differential gene expression profiling RNA-seq read count analysis 10
einverted Finds DNA inverted repeats 5
epestfind Finds PEST motifs as potential proteolytic cleavage sites 5
equicktandem Finds tandem repeats 5
est2genome Align EST and genomic DNA sequences 5
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
etandem Looks for tandem repeats in a nucleotide sequence 5
Export datasets to remote files source 1
Extract element identifiers of a list collection 2
extractfeat Extract features from a sequence 5
extractseq Extract regions from a sequence 5
Fasta Statistics display summary statistics for a FASTA file 1
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 Summary Statistics by column Sequence assembly validation 4
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
fastqillumina-to-fqtoc converter 1
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 SAM or BAM files on FLAG MAPQ RG LN or by region Filtering Nucleic acid sequence analysis 2
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 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
FPKM Count calculates raw read count, FPM, and FPKM for each gene 8
freak Residue/base frequency table or plot 5
fuzznuc Nucleic acid pattern search 6
fuzzpro Protein pattern search 5
fuzztran Protein pattern search after translation 5
garnier Predicts protein secondary structure 5
geecee Calculates fractional GC content of nucleic acid sequences 5
genbank-to-genbank.gz converter 1
genbank.gz-to-genbank converter 1
Gene Body Coverage (BAM) Read coverage over gene body. 13
Gene Body Coverage (Bigwig) Read coverage over gene body 12
Gene length and GC content from GTF and FASTA file 4
getorf Finds and extracts open reading frames (ORFs) 5
gff3.bz2-to-gff3 converter 1
goseq tests for overrepresented gene categories Gene-set enrichment analysis 12
gro-to-pdb converter 1
Group data by a column and perform aggregate operation on other columns. 4
gtf-to-interval_index converter 1
heatmap2 6
helixturnhelix Report nucleic acid binding motifs 5
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 6
HIV-Trace with options and commands 2
hmoment Hydrophobic moment calculation 5
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
HyPhy-aBSREL adaptive Branch Site Random Effects Likelihood 27
HyPhy-BGM - Detecting coevolving sites via Bayesian graphical models 26
HyPhy-BUSTED Branch-site Unrestricted Statistical Test for Episodic Diversification 26
HyPhy-CFEL Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches 6
HyPhy-Conv translate an in-frame codon alignment to proteins 5
HyPhy-FADE : FUBAR* Approach to Directional Evolution (*Fast Unconstrained Bayesian Approximation) 25
HyPhy-FEL Fixed Effects Likelihood 25
HyPhy-FUBAR Fast Unconstrained Bayesian AppRoximation 25
HyPhy-GARD Genetic Algorithm for Recombination Detection 26
HyPhy-MEME Mixed Effects Model of Evolution 25
HyPhy-PRIME Property Informed Models of Evolution 20
HyPhy-RELAX Detect relaxed selection in a codon-based phylogenetic framework 24
HyPhy-SLAC Single Likelihood Ancestor Counting 25
HyPhy-Summary generate summary report of HyPhy analyses 6
IdxStats reports stats of the BAM index file 8
iep Calculates the isoelectric point of a protein 5
inchi-to-mol converter 2
Infer Experiment speculates how RNA-seq were configured 12
infoseq Displays some simple information about sequences 5
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 12
Insert indel qualities into a BAM file 4
Insertion Profile calculates the distribution of inserted nucleotides across reads 6
IQ-TREE Phylogenomic / evolutionary tree construction from multiple sequences 7
isochore Plots isochores in large DNA sequences 5
ivar consensus Call consensus from aligned BAM file 9
ivar removereads Remove reads from trimmed BAM file 11
ivar trim Trim reads in aligned BAM 13
ivar variants Call variants from aligned BAM file 9
Join two files 12
JQ process JSON 1
Junction Annotation compares detected splice junctions to reference gene model 12
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 12
Kraken2 assign taxonomic labels to sequencing reads 5
Krona pie chart from taxonomic profile 10
LASTZ : align long sequences 7
LASTZ_D : estimate substitution scores matrix 5
lindna Draws linear maps of DNA constructs 5
Lofreq filter called variants posteriorly 4
MAFFT Multiple alignment program for amino acid or nucleotide sequences 9
MAFFT add Align a sequence,alignment or fragments to an existing alignment. 6
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
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 17
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 16
marscan Finds MAR/SAR sites in nucleic sequences 5
maskfeat Mask off features of a sequence 5
maskseq Mask off regions of a sequence 5
matcher Finds the best local alignments between two sequences 5
MeanQualityByCycle chart distribution of base qualities 14
MEGAHIT for metagenomics assembly 7
megamerger Merge two large overlapping nucleic acid sequences 5
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 14
merger Merge two overlapping nucleic acid sequences 5
MergeSamFiles merges multiple SAM/BAM datasets into one 14
metaviralSPAdes extract and assembly viral genomes from metagenomic data 6
MethylDackel A tool for processing bisulfite sequencing alignments Gene methylation analysis 7
methylKit DNA methylation analysis and annotation 1
metilene calling differentially methylated regions from bisulfite sequencing data 5
Mismatch Profile calculates the distribution of mismatches across reads 6
mol2-to-mol converter 2
mothur.ref.taxonomy-to-mothur.seq.taxonomy converter 2
msbar Mutate sequence beyond all recognition 5
Multi-Join (combine multiple files) 10
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 18
NCBI efetch Perform eFetch operation from NCBI 1
NCBI EFetch fetch records from NCBI 1
needle Needleman-Wunsch global alignment 5
neostore.zip-to-neostore converter 1
newcpgreport Report CpG rich areas 5
newcpgseek Reports CpG rich region 5
newseq Type in a short new sequence 5
Nextclade Viral genome clade assignment, mutation calling, and sequence quality checks 18
noreturn Removes carriage return from ASCII files 5
NormalizeFasta normalize fasta datasets 14
notseq Exclude a set of sequences and write out the remaining ones 5
nthseq Writes one sequence from a multiple set of sequences 5
ObservableHQ Select multiple datasets for analysis on the ObservableHQ platform 1
octanol Displays protein hydropathy 5
oddcomp Find protein sequence regions with a biased composition 5
Paired-end histogram of insert size frequency 1
palindrome Looks for inverted repeats in a nucleotide sequence 5
Pangolin Phylogenetic Assignment of Outbreak Lineages 22
pasteseq Insert one sequence into another 5
Pathview for pathway based data integration and visualization 3
patmatdb Search a protein sequence with a motif 5
pdb-to-gro converter 1
pepcoil Predicts coiled coil regions 5
pepinfo Plots simple amino acid properties in parallel 5
pepnet Displays proteins as a helical net 5
pepstats Protein statistics 5
pepwheel Shows protein sequences as helices 5
pepwindow Displays protein hydropathy 5
pepwindowall Displays protein hydropathy of a set of sequences 5
Phred means Calculate average phred scores (total) 1
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 6
plotcon Plot quality of conservation of a sequence alignment 5
plotorf Plot potential open reading frames 5
plotProfile creates a profile plot for score distributions across genomic regions 16
Pluck longest Pluck longest sequence from a group of contigs 1
polydot Displays all-against-all dotplots of a set of sequences 5
preg Regular expression search of a protein sequence 6
prettyplot Displays aligned sequences, with colouring and boxing 5
prettyseq Output sequence with translated ranges 5
primersearch Searches DNA sequences for matches with primer pairs 5
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 11
QualiMap BamQC 5
QualityScoreDistribution chart quality score distribution 14
Quast Genome assembly Quality 14
Read Distribution calculates how mapped reads were distributed over genome feature 12
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 10
Read GC determines GC% and read count 10
Read NVC to check the nucleotide composition bias 10
Read Quality determines Phred quality score 10
Realign reads with LoFreq viterbi 5
ReorderSam reorder reads to match ordering in reference sequences 17
Replace parts of text 12
Replace ambiguous codons in a multiple alignment using HyPhy 4
Replace column by values which are defined in a convert file 2
Replace Text in a specific column 11
Replace Text in entire line 11
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Resistance Gene Identifier (RGI) This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models. 1
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
RevertSam revert SAM/BAM datasets to a previous state 14
revseq Reverse and complement a sequence 5
RNA fragment size calculates the fragment size for each gene/transcript 8
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly Sequence alignment 19
RNA STARSolo mapping, demultiplexing and gene quantification for single cell RNA-seq Sequence alignment 8
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 12
Sailfish transcript quantification from RNA-seq data 4
sam-to-bam converter 1
sam-to-bigwig converter 1
sam-to-qname_sorted.bam converter 1
sam-to-unsorted.bam converter 1
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 19
Samtools ampliconclip clip primer bases from bam files 2
Samtools Chromosome Sizes order of storing aligned sequences 1
Samtools fastx extract FASTA or FASTQ from alignment files 3
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 stats generate statistics for BAM dataset 7
Samtools view - reformat, filter, or subsample SAM, BAM or CRAM 9
Search in textfiles (grep) 11
Select first lines from a dataset (head) 9
Select last lines from a dataset (tail) 9
Send to cloud 1
seqmatchall All-against-all comparison of a set of sequences 5
seqret Reads and writes sequences 5
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
showfeat Show features of a sequence 5
shuffleseq Shuffles a set of sequences maintaining composition 5
sigcleave Reports protein signal cleavage sites 5
Single ID Extract a dataset ID associated with a single dataset into a table 1
sirna Finds siRNA duplexes in mRNA 5
sixpack Display a DNA sequence with 6-frame translation and ORFs 7
skipseq Reads and writes sequences, skipping first few 5
smi-to-mol converter 2
smi-to-smi converter 2
snipit Summarise snps relative to a reference sequence 2
SnpEff eff: annotate variants for SARS-CoV-2 1
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
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 11
Sort a row according to their columns 12
SortSam sort SAM/BAM dataset 14
SPAdes genome assembler for genomes of regular and single-cell projects Genome assembly 16
Split file to dataset collection 7
splitter Split a sequence into (overlapping) smaller sequences 5
supermatcher Match large sequences against one or more other sequences 5
syco Synonymous codon usage Gribskov statistic plot 5
Table Compute computes operations on table data 4
tabular-to-csv converter 1
tac reverse a file (reverse cat) 9
tar-to-directory converter 2
tcode Fickett TESTCODE statistic to identify protein-coding DNA 5
Text reformatting with awk 13
Text transformation with sed 11
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
tmap Displays membrane spanning regions 5
TN93 Cluster sequences that lie within a specific distance of each other 2
TN93 Filter - remove sequences from a reference that are within a given distance of of a cluster 2
tranalign Align nucleic coding regions given the aligned proteins 5
Transcript Integrity Number evaluates RNA integrity at a transcript level 8
transeq Translate nucleic acid sequences 5
Trim Galore! Quality and adapter trimmer of reads 9
trimest Trim poly-A tails off EST sequences 5
trimseq Trim ambiguous bits off the ends of sequences 5
twofeat Finds neighbouring pairs of features in sequences 5
Unfold columns from a table 11
union Reads sequence fragments and builds one sequence 5
Unique occurrences of each record 9
Unique lines assuming sorted input file 11
unsorted.bam-to-bigwig converter 1
Upload File from your computer Query and retrieval 3
ValidateSamFile assess validity of SAM/BAM dataset 15
VAPOR Classify Influenza samples from short reads sequence data 4
Variant Frequency Plot Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data Aggregation 4
vcf-to-bgzip converter 2
vcf-to-bigwig converter 1
vcf-to-tabix converter 2
vcf-to-vcf_bgzip converter 1
VCF-VCFintersect: Intersect two VCF datasets 5
vcf_bgzip-to-tabix converter 2
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 6
vectorstrip Strips out DNA between a pair of vector sequences 5
water Smith-Waterman local alignment 5
wig-to-bigwig converter 1
Wiggle to Interval 2
WIP Work in progress to extract data from files 1
wobble Wobble base plot 5
wordcount Counts words of a specified size in a DNA sequence 5
wordmatch Finds all exact matches of a given size between 2 sequences 5
xtc-to-dcd converter 1