Examples : samtools, bed, topic:conversion

290 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset 3
Add input name as column to an existing tabular file 2
AddCommentsToBam add comments to BAM dataset 12
AddOrReplaceReadGroups add or replaces read group information 12
AnnotateBed annotate coverage of features from multiple files 17
AnnotatePeaks Genomic annotation of Chip-Seq peaks 2
Apply Variant Recalibration 3
Arithmetic Operations on tables 2
BAM to BED converter 19
BAM-to-SAM convert BAM to SAM 7
bamCompare normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them 16
bamCoverage generates a coverage bigWig file from a given BAM file 17
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
Base Coverage of all intervals Quantification 5
Base Recalibrator calculates covariates used to recalibrate base quality scores of reads 3
bcftools call SNP/indel variant calling from VCF/BCF 9
bcftools view Converts BCF format to VCF format 11
BED to BAM converter 17
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 16
BEDPE to BAM converter 17
BedToIntervalList convert coordinate data into picard interval list format 12
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
Bowtie2 - map reads against reference genome 21
Build custom track for UCSC genome browser 2
CEAS Annotate intervals and scores with genome features 3
Change Case of selected columns 1
CleanSam perform SAM/BAM grooming 12
ClosestBed find the closest, potentially non-overlapping interval 17
ClustalW multiple sequence alignment program for DNA or proteins 4
Cluster the intervals of a dataset Sequence clustering Sequence merging 5
ClusterBed cluster overlapping/nearby intervals 16
Collapse sequences 3
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
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
Combine Variants 3
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 17
Compute an expression on every row 4
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 17
Compute quality statistics 3
Compute quality statistics for SOLiD data 1
Compute sequence length 6
computeGCBias Determine the GC bias of your sequenced reads 16
computeMatrix prepares data for plotting a heatmap or a profile of given regions 17
Concatenate FASTA alignment by species 2
Concatenate two datasets into one dataset Aggregation 5
Concatenate datasets tail-to-head 1
Condense consecutive characters 2
Convert delimiters to TAB 1
Convert SOLiD output to fastq 1
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
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
Convert SAM to interval 2
Convert SAM to BAM 1
Convert tabular to dbnsfp 2
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Count occurrences of each record 2
Count GFF Features 2
Coverage of a set of intervals on second set of intervals Comparison Filtering 5
Create single interval as a new dataset 1
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 9
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 10
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
Cuffnorm Create normalized expression levels 4
Cuffquant Precompute gene expression levels 4
Cut columns from a table 2
Cutadapt Remove adapter sequences from Fastq/Fasta 16
Depth of Coverage on BAM files 3
Downsample SAM/BAM Downsample a file to retain a subset of the reads 12
Draw quality score boxplot 5
Draw quality score boxplot for SOLiD data 1
EstimateLibraryComplexity assess sequence library complexity from read sequences 12
Eval Variants 3
ExpandBed replicate lines based on lists of values in columns 16
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 8
Fasta to Fastq converter 1
FASTA Width formatter 3
FASTA-to-Tabular converter 4
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 6
FASTQ joiner on paired end reads Aggregation 8
FASTQ to FASTA converter Conversion 6
fastq_screen Screen for contamination 1
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 19
FastqToSam convert Fastq data into unaligned BAM 15
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 18
Fetch closest non-overlapping feature for every interval Filtering 4
Filter BAM datasets on a variety of attributes 7
Filter data on any column using simple expressions Formatting 1
Filter Combined Transcripts using tracking file 1
Filter FASTQ reads by quality score and length 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 1
Filter pileup on coverage and SNPs 2
Filter SAM on bitwise flag values 2
Filter sequences by length Filtering 7
FilterSamReads include or exclude aligned and unaligned reads and read lists 12
FIMO - Find Individual Motif Occurrences 11
FisherBed calculate Fisher statistic between two feature files 16
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 12
FlankBed create new intervals from the flanks of existing intervals 17
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 9
Genome Coverage compute the coverage over an entire genome 17
Get flanks returns flanking region/s for every gene Sequence analysis 5
GetFastaBed use intervals to extract sequences from a FASTA file 16
GFF-to-BED converter Conversion 1
Group data by a column and perform aggregate operation on other columns. 5
GroupByBed group by common cols and summarize other cols 16
Haplotype Caller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region 2
HISAT2 A fast and sensitive alignment program 17
Histogram of a numeric column 2
homer_annotatePeaks 1
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
Indel Realigner - perform local realignment 3
Infer Experiment speculates how RNA-seq were configured 9
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 9
Intersect the intervals of two datasets Filtering 5
Intersect intervals find overlapping intervals in various ways 17
JaccardBed calculate the distribution of relative distances between two files 16
Join the intervals of two datasets side-by-side Aggregation 5
Join two Datasets side by side on a specified field 4
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 16
MACS14 Model-based Analysis of ChIP-Seq (1.4.2) 3
MACS2 Model-based Analysis of ChIP-Seq 2
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 8
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 8
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 10
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 8
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 12
MACS2 filterdup Remove duplicate reads at the same position Regulatory element prediction 8
MACS2 predictd Predict 'd' or fragment size from alignment results Regulatory element prediction 8
MACS2 randsample Randomly sample number or percentage of total reads Regulatory element prediction 8
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) Regulatory element prediction 8
MakeTSSdist Get peak distribution around TSS 2
MakeWindowsBed make interval windows across a genome 17
Manipulate FASTQ reads on various attributes Sequence conversion 5
Map with Bowtie for Illumina 7
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
MapBed apply a function to a column for each overlapping interval 17
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 13
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 12
MaskFastaBed use intervals to mask sequences from a FASTA file 16
MeanQualityByCycle chart distribution of base qualities 12
MEME - Multiple Em for Motif Elicitation 1
MEME - Multiple Em for Motif Elicitation 10
Merge the overlapping intervals of a dataset Sequence merging 4
Merge BAM Files merges BAM files together 3
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 16
Merge Columns together 2
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 12
MergeBED combine overlapping/nearby intervals into a single interval 16
MergeSamFiles merges multiple SAM/BAM datasets into one 12
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
MultiCovBed counts coverage from multiple BAMs at specific intervals 16
Multiple Intersect identifies common intervals among multiple interval files 19
NormalizeFasta normalize fasta datasets 12
NucBed profile the nucleotide content of intervals in a FASTA file 17
OverlapBed computes the amount of overlap from two intervals 16
Paste two files side by side 1
Pileup-to-Interval condenses pileup format into ranges of bases 4
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 assessing 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
Preprocess files for SARTools generate design/target file and archive for SARTools inputs 5
Print Reads on BAM files 3
QualityScoreDistribution chart quality score distribution 12
RandomBed generate random intervals in a genome 17
Read Distribution calculates how mapped reads were distributed over genome feature 9
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 7
Read GC determines GC% and read count 7
Read NVC to check the nucleotide composition bias 7
Read Quality determines Phred quality score 7
Realigner Target Creator for use in local realignment 3
Reduce Reads in BAM files 3
ReldistBed calculate the distribution of relative distances 16
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
Reverse-Complement 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 12
RevertSam revert SAM/BAM datasets to a previous state 12
RmDup remove PCR duplicates 7
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly 13
RNA/DNA converter 5
RNAseqDataAnnotation tool for RNAseq data : gene length normalisation and genes annotation 1
sam-stats - Compute statistics from SAM or BAM files 2
SAM-to-BAM convert SAM to BAM 11
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 17
Samtools flagstat tabulate descriptive stats for BAM datset 8
samtools mpileup multi-way pileup of variants 9
SARTools DESeq2 Compare two or more biological conditions in a RNA-Seq framework with DESeq2 6
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
Select Variants from VCF files 3
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
ShuffleBed randomly redistrubute intervals in a genome 17
Sickle windowed adaptive trimming of FASTQ data 5
Slice BAM by genomic regions 5
SlopBed adjust the size of intervals 18
SnpEff eff: annotate variants 14
SnpSift Annotate SNPs from dbSnp 7
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 7
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
SortBED order the intervals 16
SortSam sort SAM/BAM dataset 12
SpacingBed reports the distances between features 12
Split file according to the values of a column 1
SPP SPP cross-correlation analysis package 1
Subtract the intervals of two datasets Filtering 5
Subtract Whole Dataset from another dataset 3
SubtractBed remove intervals based on overlaps 16
Tabular-to-FASTA converts tabular file to FASTA format 3
TagBed tag BAM alignments based on overlaps with interval files 16
TopHat Gapped-read mapper for RNA-seq data 10
TopHat for Illumina Find splice junctions using RNA-seq data 3
Trim leading or trailing characters 1
Trim sequences 5
Unified Genotyper SNP and indel caller 3
Union of two datasets based on common field 1
Upload File from your computer 2
Validate Variants 2
ValidateSamFile assess validity of SAM/BAM dataset 12
Variant Annotator 3
Variant Filtration on VCF files 3
Variant Recalibrator 3
Wiggle to Interval 2
WigMaker for BED files 1
WindowBed find overlapping intervals within a window around an interval 16
Zip and name files 2