378 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset 3
Analyze Covariates - draw plots 2
Annotate a VCF dataset with custom filters 2
AnnotateBed annotate coverage of features from multiple files 16
ANNOVAR Annotate VCF with functional information using ANNOVAR 2
Apply Variant Recalibration 2
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 BED converter 20
BAM-to-SAM convert BAM to SAM 7
BamLeftAlign indels in BAM datasets 7
Bar chart for multiple columns 1
Barcode Splitter 5
Base Coverage of all intervals Quantification 5
bcftools call SNP/indel variant calling from VCF/BCF 6
bcftools mpileup Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files 2
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 9
BED to BAM converter 17
BED to IGV create batch script for taking IGV screenshots 9
bed to protein map genomic location of proteins for MVP 1
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 16
BedCov calculate read depth for a set of genomic intervals 3
BEDPE to BAM converter 17
BLAST XML to selected tabular columns Convert BLAST XML output to tabular 1
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 15
Bowtie2 - map reads against reference genome 21
Boxplot of quality statistics 1
Build base quality distribution 2
Build custom track for UCSC genome browser 3
CalMD recalculate MD/NM tags 2
Change Case of selected columns 1
Clip adapter sequences 5
ClosestBed find the closest, potentially non-overlapping interval 16
CloudMap: Check snpEff Candidates Marks up a snpEff output file with matches to a gene candidate list. 1
CloudMap: EMS Variant Density Mapping Map a mutation by linkage to regions of high mutation density using WGS data 2
CloudMap: Hawaiian Variant Mapping with WGS data Map a mutation by plotting recombination frequencies resulting from crossing to a highly polymorphic strain 2
CloudMap: in silico complementation Perform in silico complementation analysis on multiple tabular snpEff output files 1
CloudMap: Variant Discovery Mapping with WGS data Map a mutation using in silico bulk segregant linkage analysis using variants that are already present in the mutant strain of interest (rather than those introduced by a cross to a polymorphic strain). 2
Cluster the intervals of a dataset Sequence clustering Sequence merging 5
ClusterBed cluster overlapping/nearby intervals 16
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
Collapse sequences 4
Column Regex Find And Replace 3
Combine FASTA and QUAL into FASTQ 3
Combine Variants 2
Compare two Datasets to find common or distinct rows 1
Complement intervals of a dataset Sequence coordinate conversion 6
ComplementBed Extract intervals not represented by an interval file 17
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) 17
Compute quality statistics 4
Concatenate two datasets into one dataset Aggregation 6
Concatenate FASTA alignment by species 2
Concatenate datasets tail-to-head 1
Concatenate multiple datasets tail-to-head 1
Convert delimiters to TAB 1
Convert BCF to BCF_BGZIP 1
Convert BCF_BGZIP to BCF 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 fai file 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 gffCompare annotated GTF to BED for StringTie results 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 Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 1
Convert SAM to interval 2
Convert SAM to BAM 1
Convert tabular to dbnsfp 1
Convert, Merge, Randomize BAM datasets and perform other transformations 4
Correlation for numeric columns 2
Count occurrences of each record 1
Count Covariates on BAM files 2
Count intervals in one file overlapping intervals in another file 3
Coverage of a set of intervals on second set of intervals Comparison Filtering 5
CRAVAT Submit, Check, and Retrieve Submits, checks for, and retrieves data for cancer annotation 1
CRAVAT-P Submit, Intersect, Check, and Retrieve | Submits, intersects, checks for, and retrieves data for cancer annotation. 1
Create a BedGraph of genome coverage 4
Create a histogram of genome coverage 4
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
CustomProDB Generate protein FASTAs from exosome or transcriptome data 1
Cut columns from a table 2
Depth of Coverage on BAM files 2
DESeq2 Determines differentially expressed features from count tables Differential gene expression analysis 14
Draw nucleotides distribution chart 4
Draw quality score boxplot 5
Draw ROC plot on "Perform LDA" output 3
edgeR Perform differential expression of count data 3
Eval Variants 2
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 7
Extract MAF blocks given a set of genomic intervals 1
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
Extract reads in SAM format from NCBI SRA. 11
Extract reads in FASTQ/A format from NCBI SRA. 11
Extract reads in BAM format from NCBI SRA. 1
FASTA from allele counts Generate major and minor allele sequences from alleles table 1
FASTA Merge Files and Filter Unique Sequences Concatenate FASTA database files together 3
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 Masker by quality score 3
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads 3
FASTQ Summary Statistics by column 2
FASTQ to FASTA converter 4
FASTQ to Tabular converter 4
FASTQ Trimmer by column 4
FastQC:Read QC reports using FastQC Sequence composition calculation Sequencing quality control Statistical calculation 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 by quality 5
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 MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
Filter pileup on coverage and SNPs 3
Filter SAM on bitwise flag values 2
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 5
Filter sequences by length Filtering 5
Filter Tabular 4
FisherBed calculate Fisher statistic between two feature files 16
Flagstat tabulate descriptive stats for BAM datset 7
FlankBed create new intervals from the flanks of existing intervals 17
FreeBayes bayesian genetic variant detector 7
Gene BED To Exon/Intron/Codon BED expander 1
Generate A Matrix for using PC and LDA 2
Generate pileup from BAM dataset 3
Generate pileup format from NCBI sra. 10
Genome Coverage compute the coverage over an entire genome 17
Get flanks returns flanking region/s for every gene Sequence analysis 5
Get Microbial Data 1
GetFastaBed use intervals to extract sequences from a FASTA file 16
GFF-to-BED converter Conversion 1
GffCompare compare assembled transcripts to a reference annotation 1
gffread Filters and/or converts GFF3/GTF2 records 3
GMAJ Multiple Alignment Viewer 1
Group data by a column and perform aggregate operation on other columns. 2
GroupByBed group by common cols and summarize other cols 16
GTF-to-BEDGraph converter Conversion 1
HISAT2 A fast and sensitive alignment program 14
Histogram of a numeric column 4
idconvert Convert mass spectrometry identification files 2
idpAssemble Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels. 2
idpEmbedder Embed human/mouse gene metadata into IDPicker files 2
idpQonvert Prepare identification results for IDPicker 2
idpQuery Creates text reports from idpDB files. 2
IdxStats tabulate mapping statistics for BAM dataset 8
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Indel Realigner - perform local realignment 2
Intersect the intervals of two datasets Filtering 7
Intersect BAM alignments with intervals in another files 3
Intersect intervals find overlapping intervals in various ways 16
Intersect multiple sorted BED files 20
JaccardBed calculate the distribution of relative distances between two files 16
Join the intervals of two datasets side-by-side Aggregation 5
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 2
Lastz map short reads against reference sequence 5
LAV to BED Converts a LAV formatted file to BED format 1
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 16
MAF Coverage Stats Alignment coverage information 1
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
MakeWindowsBed make interval windows across a genome 17
Manipulate FASTQ reads on various attributes 3
Map with BWA - map short reads (< 100 bp) against reference genome 14
Map with BWA for Illumina 4
Map with BWA for SOLiD 3
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 16
MapBed apply a function to a column for each overlapping interval 16
MaskFastaBed use intervals to mask sequences from a FASTA file 16
Megablast compare short reads against htgs, nt, and wgs databases 3
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 16
Merge BedGraph files 4
Merge Columns together 2
MergeBED combine overlapping/nearby intervals into a single interval 16
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
MPileup call variants 10
MS-GF+ Identifies peptides in tandem mass spectra using the MS-GF+ search engine. 5
msconvert Convert and/or filter mass spectrometry files 2
msconvert Convert and filter a mass spec peak list 1
msconvert (vendor support) Convert and/or filter mass spectrometry files (with vendor support on Windows) 1
msconvert RAW Convert and filter a Thermo Finnigan RAW file 1
msconvert Subset Peak List against list of scan numbers or indices. 1
MultiCovBed counts coverage from multiple BAMs at specific intervals 16
multiqc aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 8
MyriMatch Identify peptides in tandem mass spectra. 2
mz to sqlite Extract mzIdentML and associated proteomics datasets into a SQLite DB 1
Naive Variant Caller - tabulate variable sites from BAM datasets 4
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 15
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 11
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 15
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 13
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 16
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 9
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 14
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 14
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 11
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NucBed profile the nucleotide content of intervals in a FASTA file 16
OverlapBed computes the amount of overlap from two intervals 16
Parse blast XML output 2
Paste two files side by side 1
PepPointer classify genomic location of peptides 3
Peptide Genomic Coordinate Get genomic location/coordinate of peptides using mzsqlite DB and genomic mapping sqlite DB 1
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 10
Perform LDA Linear Discriminant Analysis 3
Pileup-to-Interval condenses pileup format into ranges of bases 5
Plotting tool for multiple series and graph types 4
Print Reads from BAM files 3
Protein Database Downloader 2
PSM to SAM Generate SAM files from PSMs. 1
Quality format converter (ASCII-Numeric) 4
QuanTP Correlation between protein and transcript abundances 1
Query Tabular using sqlite sql 8
RandomBed generate random intervals in a genome 17
Realigner Target Creator for use in local realignment 2
Regex Find And Replace 2
Reheader copy SAM/BAM header between datasets 2
ReldistBed calculate the distribution of relative distances 16
Remove beginning of a file 1
Remove sequencing artifacts 5
Rename sequences 5
Reverse Complement a MAF file 1
Reverse-Complement 5
RmDup remove PCR duplicates 7
RNA/DNA converter 5
SAM-to-BAM convert SAM to BAM 10
SAM/BAM to count matrix using HTSeq code 1
Scatterplot of two numeric columns 5
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Search GUI Perform protein identification using various search engines and prepare results for input to Peptide Shaker 12
Secure Hash / Message Digest on a dataset 1
Select lines that match an expression 1
Select first lines from a dataset 1
Select high quality segments 3
Select last lines from a dataset 1
Select random lines from a file 2
Select Variants from VCF files 3
SFF converter 1
ShuffleBed randomly redistrubute intervals in a genome 17
Slice BAM by genomic regions 6
Slice VCF to get data from selected regions 2
SlopBed adjust the size of intervals 17
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
SnpEff Variant efefct and annotation 14
SnpEff Download Download a new database 14
SnpSift Annotate Annotate SNPs from dbSnp 8
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 8
SnpSift Filter Filter variants using arbitrary expressions 8
SnpSift Intervals Filter variants using intervals 8
Sort BAM dataset 7
Sort data in ascending or descending order 2
SortBED order the intervals 16
SpacingBed reports the distances between features 12
Split BAM datasets on variety of attributes 4
Split BAM dataset on readgroups 2
Split MAF blocks by Species 1
SQLite to tabular for SQL query 4
Stats generate statistics for BAM dataset 4
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 12
StringTie merge transcripts 6
Subtract the intervals of two datasets Filtering 7
Subtract Whole Dataset from another dataset 3
SubtractBed remove intervals based on overlaps 16
Summary Statistics for any numerical column 3
Table Recalibration on BAM files 1
Tabular to FASTQ converter 4
Tabular-to-FASTA converts tabular file to FASTA format 2
TagBed tag BAM alignments based on overlaps with interval files 16
TopHat Gapped-read mapper for RNA-seq data 12
Tophat Fusion Post post-processing to identify fusion genes 1
Translate BED transcripts cDNA in 3frames or CDS 1
Trim leading or trailing characters 1
Trim sequences 6
Unified Genotyper SNP and indel caller 2
Upload File from your computer 2
Validate Variants 2
Variant Annotator 2
Variant Annotator process variant counts 2
Variant Filtration on VCF files 2
Variant Recalibrator 3
Varscan for variant detection 3
VCF to MAF Custom Track for display at UCSC 1
VCF-BEDintersect: Intersect VCF and BED datasets 6
VCF-VCFintersect: Intersect two VCF datasets 7
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 7
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 6
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 7
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 6
VCFcheck: Verify that the reference allele matches the reference genome 6
VCFcombine: Combine multiple VCF datasets 7
VCFcommonSamples: Output records belonging to samples common between two datasets 6
VCFdistance: Calculate distance to the nearest variant 6
VCFfilter: filter VCF data in a variety of attributes 5
VCFfixup: Count the allele frequencies across alleles present in each record in the VCF file 5
VCFflatten: Removes multi-allelic sites by picking the most common alternate 5
VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles 7
VCFgenotypes: Convert numerical representation of genotypes to allelic 6
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 6
VCFleftAlign: Left-align indels and complex variants in VCF dataset 6
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 7
VCFselectsamples: Select samples from a VCF dataset 7
VCFsort: Sort VCF dataset by coordinate 5
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 8
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1
WindowBed find overlapping intervals within a window around an interval 16