256 tool(s) found

Tool Description Topics Available version(s)
16S rRNA Search Similarity Search 1
Add column to an existing dataset 3
AddCommentsToBam add comments to BAM dataset 9
AddOrReplaceReadGroups add or replaces read group information 9
AnnotateBed annotate coverage of features from multiple files 16
awk 1
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
Bar chart for multiple columns 1
BED to BAM converter 17
BED-to-bigBed converter Conversion 2
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 9
Bowtie2 align Align reads to db 1
Bowtie2 build Create bowtie2 index for hg38 and phiX174 fasta 1
Boxplot of quality statistics 1
bsfcall Mapping bisulfite-seq reads and calling methylated cytosines 1
CalculateEntropyDiv Calculate entropy 1
Change Case of selected columns 1
CleanSam perform SAM/BAM grooming 9
ClosestBed find the closest, potentially non-overlapping interval 16
ClusterBed cluster overlapping/nearby intervals 16
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
COG Search Similarity Search 1
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 9
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 9
CollectGcBiasMetrics charts the GC bias metrics 9
CollectInsertSizeMetrics plots distribution of insert sizes 9
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 10
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 9
ComMet Detection of differentially methylated regions from bisulfite-seq mapping data 1
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 17
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 17
Concatenate 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 len file 1
Convert FASTA to Tabular 1
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 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
Count occurrences of each record 1
Create single interval as a new dataset 1
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
Cut columns from a table 2
Cut Cut sequence 1
Cutadapt Trim adapter 1
Detect_Indels Detect InDels 1
Detect_SNPs Detect SNPs 1
Download References Data for Pitagora-Galaxy 1
Downsample SAM/BAM Downsample a file to retain a subset of the reads 9
Edit Header 1
Elapsed time of each job 1
EstimateLibraryComplexity assess sequence library complexity from read sequences 9
Exclude_N_Fastq2 Exclude Ns 1
ExpandBed replicate lines based on lists of values in columns 16
Export to a Local File 2
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
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
FastQC:Read QC reports using FastQC Sequence composition calculation Sequencing quality control Statistical calculation 16
FastqMcf sequence quality filtering and clipping 2
FastqToSam convert Fastq data into unaligned BAM 12
Filter data on any column using simple expressions Formatting 1
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
FilterSamReads include or exclude aligned and unaligned reads and read lists 9
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 9
FlankBed create new intervals from the flanks of existing intervals 17
Gatk 3.3 binary loader Upload GATK3.3 to Pitagora galaxy system. 1
Gatk 3.3 variant caller GATK 3.3 based variant call system. 1
GATK resource bundle downloader GATK resource bundle downloader. 1
Gene BED To Exon/Intron/Codon BED expander 1
Generate pileup format from NCBI sra. 10
Genome Coverage compute the coverage over an entire genome 17
Get Microbial Data 1
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. 2
GroupByBed group by common cols and summarize other cols 16
GTF-to-BEDGraph converter Conversion 1
Import a Local File 1
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
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
JellyfishCount Count K-mer 1
JellyfishDump Dump K-mer 1
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
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
MACS Model-based Analysis of ChIP-Seq 4
MACS14 Model-based Analysis of ChIP-Seq (1.4.2) 5
MACS2 bdgbroadcall Call broad peaks from bedGraph output Regulatory element prediction 7
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph Regulatory element prediction 7
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files Regulatory element prediction 8
MACS2 bdgpeakcall Call peaks from bedGraph output Regulatory element prediction 7
MACS2 callpeak Call peaks from alignment results Regulatory element prediction 10
MACS2 filterdup Remove duplicate reads at the same position Regulatory element prediction 7
MACS2 predictd Predict 'd' or fragment size from alignment results Regulatory element prediction 7
MACS2 randsample Randomly sample number or percentage of total reads Regulatory element prediction 7
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) Regulatory element prediction 7
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
Map with BWA for Illumina 4
Map with BWA for SOLiD 3
MapBed apply a function to a column for each overlapping interval 16
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 9
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 9
MaskFastaBed use intervals to mask sequences from a FASTA file 16
MeanQualityByCycle chart distribution of base qualities 9
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 16
Merge Columns together 2
Merge(final) Output final reports 1
Merge_SNPs_/_InDels_data_files Merge SNPs / InDels data files 1
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 9
MergeBED combine overlapping/nearby intervals into a single interval 16
MergeSamFiles merges multiple SAM/BAM datasets into one 9
MetaGeneAnotator find ORFs 1
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
MultiCovBed counts coverage from multiple BAMs at specific intervals 16
NormalizeFasta normalize fasta datasets 9
NucBed profile the nucleotide content of intervals in a FASTA file 16
OverlapBed computes the amount of overlap from two intervals 16
Paste two files side by side 1
PhixRemove Remove phiX174 1
Qual_Filter_FASTQFASTA Quality filter 1
QualityScoreDistribution chart quality score distribution 9
RandomBed generate random intervals in a genome 17
RefSeq Search Similarity Search 1
ReldistBed calculate the distribution of relative distances 16
Remove beginning of a file 1
ReorderSam reorder reads to match ordering in reference sequences 12
ReplaceSamHeader replace header in a SAM/BAM dataset 12
Report(interim) Output interim reports 1
Reverse Complement a MAF file 1
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 9
RevertSam revert SAM/BAM datasets to a previous state 9
RNAmmer 1.2 find rRNAs 1
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 2
Sailfish transcript quantification from RNA-seq data 1
SAM-to-BAM convert SAM to BAM 10
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 12
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Secure Hash / Message Digest on a dataset 1
sed 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
SFF converter 1
ShuffleBed randomly redistrubute intervals in a genome 17
SICER Statistical approach for the Identification of ChIP-Enriched Regions 1
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 effect and annotation 1
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
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 9
Split MAF blocks by Species 1
SQL Runner (SQLite) 1
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
SubtractBed remove intervals based on overlaps 16
Summary Statistics for any numerical column 3
Tabular to CSV converter 1
TagBed tag BAM alignments based on overlaps with interval files 16
TopHat Gapped-read mapper for RNA-seq data 12
TrEMBL Search Similarity Search 1
Trim leading or trailing characters 1
Trinity De novo assembly of RNA-Seq data Using Trinity EST assembly 5
tRNAscan-SE 1.23 find tRNAs 1
Unannotated Extract not annotated sequences 1
Upload File from your computer 2
ValidateSamFile assess validity of SAM/BAM dataset 9
VCF to MAF Custom Track for display at UCSC 1
Visualize distribution of DNA polymorphism 1
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