Examples : samtools, bed, topic:conversion

275 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 1
AddCommentsToBam add comments to BAM dataset 11
AddOrReplaceReadGroups add or replaces read group information 11
AnnotateBed annotate coverage of features from multiple files 17
AnnotatePeaks Genomic annotation of Chip-Seq peaks 2
Apply Variant Recalibration 4
Arithmetic Operations on tables 2
BAM to BED converter 21
BAM-to-SAM convert BAM to SAM 8
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 16
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 4
bcftools call SNP/indel variant calling from VCF/BCF 7
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 9
BED to BAM converter 18
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 17
BEDPE to BAM converter 18
BedToIntervalList convert coordinate data into picard interval list format 11
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
Bowtie2 - map reads against reference genome 22
Build custom track for UCSC genome browser 3
CEAS Annotate intervals and scores with genome features 1
Change Case of selected columns 1
CleanSam perform SAM/BAM grooming 11
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 17
Collapse sequences 4
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 11
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 11
CollectGcBiasMetrics charts the GC bias metrics 11
CollectInsertSizeMetrics plots distribution of insert sizes 11
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 12
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 11
Combine Variants 4
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 18
Compute an expression on every row 3
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 18
Compute quality statistics 4
Compute quality statistics for SOLiD data 1
Compute sequence length 5
computeGCBias Determine the GC bias of your sequenced reads 16
computeMatrix prepares data for plotting a heatmap or a profile of given regions 16
Concatenate FASTA alignment by species 2
Concatenate two datasets into one dataset Aggregation 6
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 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 len file 1
Convert FASTA to Tabular 1
Convert from BAM to FastQ 14
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert SAM to interval 2
Convert SAM to BAM 1
Convert tabular to dbnsfp 1
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Count occurrences of each record 2
Count GFF Features 3
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 14
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 13
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 11
Cuffmerge merge together several Cufflinks assemblies 12
Cuffnorm Create normalized expression levels 5
Cuffquant Precompute gene expression levels 5
Cut columns from a table 2
Cutadapt Remove adapter sequences from Fastq/Fasta 13
Depth of Coverage on BAM files 4
Downsample SAM/BAM Downsample a file to retain a subset of the reads 11
Draw quality score boxplot 5
Draw quality score boxplot for SOLiD data 1
EstimateLibraryComplexity assess sequence library complexity from read sequences 11
Eval Variants 4
ExpandBed replicate lines based on lists of values in columns 17
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
Fasta to Fastq converter 1
FASTA Width formatter 4
FASTA-to-Tabular converter 3
FASTQ Groomer convert between various FASTQ quality formats 4
FASTQ joiner on paired end reads 6
FASTQ to FASTA converter 4
fastq_screen Screen for contamination 1
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 17
FastqToSam convert Fastq data into unaligned BAM 14
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 16
Fetch closest non-overlapping feature for every interval Filtering 4
Filter BAM datasets on a variety of attributes 6
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 4
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 3
Filter SAM on bitwise flag values 2
Filter sequences by length Filtering 5
FilterSamReads include or exclude aligned and unaligned reads and read lists 11
FIMO - Find Individual Motif Occurrences 9
FisherBed calculate Fisher statistic between two feature files 17
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 11
Flagstat tabulate descriptive stats for BAM datset 8
FlankBed create new intervals from the flanks of existing intervals 18
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 11
Genome Coverage compute the coverage over an entire genome 18
Get flanks returns flanking region/s for every gene Sequence analysis 5
GetFastaBed use intervals to extract sequences from a FASTA file 17
GFF-to-BED converter Conversion 1
Group data by a column and perform aggregate operation on other columns. 3
GroupByBed group by common cols and summarize other cols 17
Haplotype Caller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region 3
HISAT2 A fast and sensitive alignment program 16
Histogram of a numeric column 4
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 4
Infer Experiment speculates how RNA-seq were configured 11
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 11
Intersect the intervals of two datasets Filtering 7
Intersect intervals find overlapping intervals in various ways 17
JaccardBed calculate the distribution of relative distances between two files 17
Join the intervals of two datasets side-by-side Aggregation 5
Join two Datasets side by side on a specified field 3
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 17
MACS14 Model-based Analysis of ChIP-Seq (1.4.2) 5
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 9
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 8
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 11
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 18
Manipulate FASTQ reads on various attributes 3
Map with Bowtie for Illumina 8
Map with BWA - map short reads (< 100 bp) against reference genome 15
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 17
MapBed apply a function to a column for each overlapping interval 17
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 11
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 11
MaskFastaBed use intervals to mask sequences from a FASTA file 17
MeanQualityByCycle chart distribution of base qualities 11
MEME - Multiple Em for Motif Elicitation 1
MEME - Multiple Em for Motif Elicitation 10
Merge the overlapping intervals of a dataset Sequence merging 5
Merge BAM Files merges BAM files together 3
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 17
Merge Columns together 2
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 11
MergeBED combine overlapping/nearby intervals into a single interval 17
MergeSamFiles merges multiple SAM/BAM datasets into one 11
MPileup call variants 10
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 17
Multiple Intersect identifies common intervals among multiple interval files 21
NormalizeFasta normalize fasta datasets 11
NucBed profile the nucleotide content of intervals in a FASTA file 17
OverlapBed computes the amount of overlap from two intervals 17
Paste two files side by side 1
Pileup-to-Interval condenses pileup format into ranges of bases 5
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 16
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 4
QualityScoreDistribution chart quality score distribution 11
RandomBed generate random intervals in a genome 18
Read Distribution calculates how mapped reads were distributed over genome feature 11
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 9
Read GC determines GC% and read count 9
Read NVC to check the nucleotide composition bias 9
Read Quality determines Phred quality score 9
Realigner Target Creator for use in local realignment 4
Reduce Reads in BAM files 4
ReldistBed calculate the distribution of relative distances 17
Remove beginning of a file 1
ReorderSam reorder reads to match ordering in reference sequences 14
ReplaceSamHeader replace header in a SAM/BAM dataset 14
Reverse-Complement 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 11
RevertSam revert SAM/BAM datasets to a previous state 11
RmDup remove PCR duplicates 8
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 3
SAM-to-BAM convert SAM to BAM 11
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 14
SARTools DESeq2 Compare two or more biological conditions in a RNA-Seq framework with DESeq2 6
Secure Hash / Message Digest on a dataset 1
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 4
ShuffleBed randomly redistrubute intervals in a genome 18
Sickle windowed adaptive trimming of FASTQ data 5
Slice BAM by genomic regions 6
SlopBed adjust the size of intervals 18
SnpEff Variant effect and annotation 15
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 9
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 2
SortBED order the intervals 17
SortSam sort SAM/BAM dataset 11
SpacingBed reports the distances between features 13
Split file according to the values of a column 2
SPP SPP cross-correlation analysis package 1
Subtract the intervals of two datasets Filtering 7
Subtract Whole Dataset from another dataset 3
SubtractBed remove intervals based on overlaps 17
Tabular-to-FASTA converts tabular file to FASTA format 2
TagBed tag BAM alignments based on overlaps with interval files 17
TopHat Gapped-read mapper for RNA-seq data 12
TopHat for Illumina Find splice junctions using RNA-seq data 3
Trim leading or trailing characters 1
Trim sequences 6
Unified Genotyper SNP and indel caller 4
Union of two datasets based on common field 1
Upload File from your computer 2
Validate Variants 3
ValidateSamFile assess validity of SAM/BAM dataset 11
Variant Annotator 4
Variant Filtration on VCF files 4
Variant Recalibrator 4
Wiggle to Interval 1
WigMaker for BED files 1
WindowBed find overlapping intervals within a window around an interval 17
Zip and name files 3