16S rRNA Search |
Similarity Search |
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1 |
Add column |
to an existing dataset |
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3 |
AddCommentsToBam |
add comments to BAM dataset |
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11 |
AddOrReplaceReadGroups |
add or replaces read group information |
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11 |
AnnotateBed |
annotate coverage of features from multiple files |
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17 |
awk |
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1 |
AXT to concatenated FASTA |
Converts an AXT formatted file to a concatenated FASTA alignment |
Conversion
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1 |
AXT to FASTA |
Converts an AXT formatted file to FASTA format |
Conversion
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1 |
AXT to LAV |
Converts an AXT formatted file to LAV format |
Conversion
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1 |
BAM to BED |
converter |
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21 |
BAM-to-SAM |
convert BAM to SAM |
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8 |
Bar chart |
for multiple columns |
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1 |
BED to BAM |
converter |
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18 |
BED-to-bigBed |
converter |
Conversion
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2 |
BED-to-GFF |
converter |
Conversion
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1 |
BED12 to BED6 |
converter |
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17 |
BEDPE to BAM |
converter |
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18 |
BedToIntervalList |
convert coordinate data into picard interval list format |
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11 |
Bowtie2 align |
Align reads to db |
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1 |
Bowtie2 build |
Create bowtie2 index for hg38 and phiX174 fasta |
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1 |
Boxplot |
of quality statistics |
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2 |
bsfcall |
Mapping bisulfite-seq reads and calling methylated cytosines |
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1 |
CalculateEntropyDiv |
Calculate entropy |
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1 |
Change Case |
of selected columns |
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1 |
CleanSam |
perform SAM/BAM grooming |
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11 |
ClosestBed |
find the closest, potentially non-overlapping interval |
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17 |
ClusterBed |
cluster overlapping/nearby intervals |
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17 |
CML to InChI |
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2 |
CML to mol2 |
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2 |
CML to SDF |
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2 |
CML to SMILES |
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2 |
COG Search |
Similarity Search |
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1 |
Collect Alignment Summary Metrics |
writes a file containing summary alignment metrics |
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11 |
CollectBaseDistributionByCycle |
charts the nucleotide distribution per cycle in a SAM or BAM dataset |
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11 |
CollectGcBiasMetrics |
charts the GC bias metrics |
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11 |
CollectInsertSizeMetrics |
plots distribution of insert sizes |
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11 |
CollectRnaSeqMetrics |
collect metrics about the alignment of RNA to various functional classes of loci in the genome |
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12 |
CollectWgsMetrics |
compute metrics for evaluating of whole genome sequencing experiments |
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11 |
ComMet |
Detection of differentially methylated regions from bisulfite-seq mapping data |
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1 |
Compare two Datasets |
to find common or distinct rows |
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1 |
ComplementBed |
Extract intervals not represented by an interval file |
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18 |
Compute both the depth and breadth of coverage |
of features in file B on the features in file A (bedtools coverage) |
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18 |
Concatenate datasets |
tail-to-head |
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1 |
Convert |
delimiters to TAB |
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1 |
Convert BCF to BCF_BGZIP |
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1 |
Convert BCF_BGZIP to BCF |
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1 |
Convert BED to Feature Location Index |
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1 |
Convert BED to GFF |
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1 |
Convert FASTA to 2bit |
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2 |
Convert FASTA to Bowtie base space Index |
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1 |
Convert FASTA to Bowtie color space Index |
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1 |
Convert FASTA to len file |
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1 |
Convert FASTA to Tabular |
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1 |
Convert Genomic Intervals To BED |
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1 |
Convert Genomic Intervals To Coverage |
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2 |
Convert Genomic Intervals To Strict BED |
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1 |
Convert Genomic Intervals To Strict BED12 |
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1 |
Convert Genomic Intervals To Strict BED6 |
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1 |
Convert GFF to BED |
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1 |
Convert GFF to Feature Location Index |
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1 |
Convert Len file to Linecount |
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1 |
Convert lped to fped |
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1 |
Convert lped to plink pbed |
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1 |
Convert MAF to Fasta |
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1 |
Convert MAF to Genomic Intervals |
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1 |
Convert Picard Interval List to BED6 |
converter |
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1 |
Convert plink pbed to ld reduced format |
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1 |
Convert plink pbed to linkage lped |
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1 |
Convert Ref taxonomy to Seq Taxonomy |
converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format |
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1 |
Convert SAM |
to interval |
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2 |
Convert SAM to BAM |
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1 |
Convert tabular to dbnsfp |
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1 |
Count |
occurrences of each record |
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2 |
Create single interval |
as a new dataset |
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1 |
Cuffdiff |
find significant changes in transcript expression, splicing, and promoter use |
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13 |
Cufflinks |
transcript assembly and FPKM (RPKM) estimates for RNA-Seq data |
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11 |
Cuffmerge |
merge together several Cufflinks assemblies |
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12 |
Cut |
columns from a table |
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2 |
Cut |
Cut sequence |
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1 |
Cutadapt |
Trim adapter |
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1 |
Detect_Indels |
Detect InDels |
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1 |
Detect_SNPs |
Detect SNPs |
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1 |
Download and Extract Reads in BAM |
format from NCBI SRA |
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12 |
Download and Extract Reads in FASTA/Q |
format from NCBI SRA |
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12 |
Download and Generate Pileup Format |
from NCBI SRA |
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11 |
Download References |
Data for Pitagora-Galaxy |
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1 |
Downsample SAM/BAM |
Downsample a file to retain a subset of the reads |
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11 |
Edit Header |
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1 |
Elapsed time |
of each job |
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1 |
EstimateLibraryComplexity |
assess sequence library complexity from read sequences |
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11 |
Exclude_N_Fastq2 |
Exclude Ns |
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1 |
ExpandBed |
replicate lines based on lists of values in columns |
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17 |
Export |
to a Local File |
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2 |
Extract features |
from GFF data |
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1 |
Extract Genomic DNA |
using coordinates from assembled/unassembled genomes |
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7 |
Extract MAF by block number |
given a set of block numbers and a MAF file |
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1 |
Extract Pairwise MAF blocks |
given a set of genomic intervals |
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1 |
FastQC |
Read Quality reports |
Sequence composition calculation
Sequencing quality control
Statistical calculation
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17 |
FastqMcf |
sequence quality filtering and clipping |
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2 |
FastqToSam |
convert Fastq data into unaligned BAM |
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14 |
Filter |
data on any column using simple expressions |
Formatting
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1 |
Filter GFF data by attribute |
using simple expressions |
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3 |
Filter GFF data by feature count |
using simple expressions |
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2 |
Filter GTF data by attribute values_list |
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1 |
Filter MAF |
by specified attributes |
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1 |
Filter MAF blocks |
by Size |
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1 |
Filter MAF blocks |
by Species |
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1 |
FilterSamReads |
include or exclude aligned and unaligned reads and read lists |
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11 |
FisherBed |
calculate Fisher statistic between two feature files |
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17 |
FixMateInformation |
ensure that all mate-pair information is in sync between each read and it's mate pair |
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11 |
FlankBed |
create new intervals from the flanks of existing intervals |
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18 |
Gatk 3.3 binary loader |
Upload GATK3.3 to Pitagora galaxy system. |
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1 |
Gatk 3.3 variant caller |
GATK 3.3 based variant call system. |
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1 |
GATK resource bundle downloader |
GATK resource bundle downloader. |
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1 |
Gene BED To Exon/Intron/Codon BED |
expander |
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1 |
Genome Coverage |
compute the coverage over an entire genome |
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18 |
Get Microbial Data |
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1 |
GetFastaBed |
use intervals to extract sequences from a FASTA file |
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17 |
GFF-to-BED |
converter |
Conversion
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1 |
Group |
data by a column and perform aggregate operation on other columns. |
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3 |
GroupByBed |
group by common cols and summarize other cols |
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17 |
GTF-to-BEDGraph |
converter |
Conversion
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1 |
Import |
a Local File |
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1 |
InChI to CML |
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2 |
InChI to MOL |
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2 |
InChI to MOL2 |
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2 |
InChI to SDF |
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2 |
InChI to SMILES |
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2 |
Intersect intervals |
find overlapping intervals in various ways |
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17 |
JaccardBed |
calculate the distribution of relative distances between two files |
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17 |
JellyfishCount |
Count K-mer |
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1 |
JellyfishDump |
Dump K-mer |
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1 |
Join |
the intervals of two datasets side-by-side |
Aggregation
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5 |
Join MAF blocks |
by Species |
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1 |
Join two Datasets |
side by side on a specified field |
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3 |
LAV to BED |
Converts a LAV formatted file to BED format |
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1 |
Line/Word/Character count |
of a dataset |
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1 |
LinksBed |
create a HTML page of links to UCSC locations |
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17 |
MACS |
Model-based Analysis of ChIP-Seq |
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4 |
MACS14 |
Model-based Analysis of ChIP-Seq (1.4.2) |
|
5 |
MACS2 bdgbroadcall |
Call broad peaks from bedGraph output |
Regulatory element prediction
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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
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11 |
MACS2 filterdup |
Remove duplicate reads at the same position |
Regulatory element prediction
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8 |
MACS2 predictd |
Predict 'd' or fragment size from alignment results |
Regulatory element prediction
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8 |
MACS2 randsample |
Randomly sample number or percentage of total reads |
Regulatory element prediction
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8 |
MACS2 refinepeak |
Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) |
Regulatory element prediction
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8 |
MAF Coverage Stats |
Alignment coverage information |
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1 |
MAF to BED |
Converts a MAF formatted file to the BED format |
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1 |
MAF to FASTA |
Converts a MAF formatted file to FASTA format |
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1 |
MAF to Interval |
Converts a MAF formatted file to the Interval format |
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1 |
MakeWindowsBed |
make interval windows across a genome |
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18 |
Map with BWA for Illumina |
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4 |
Map with BWA for SOLiD |
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3 |
MapBed |
apply a function to a column for each overlapping interval |
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17 |
MarkDuplicates |
examine aligned records in BAM datasets to locate duplicate molecules |
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11 |
MarkDuplicatesWithMateCigar |
examine aligned records in BAM datasets to locate duplicate molecules |
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11 |
MaskFastaBed |
use intervals to mask sequences from a FASTA file |
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17 |
MeanQualityByCycle |
chart distribution of base qualities |
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11 |
Merge BedGraph files |
combines coverage intervals from multiple BEDGRAPH files |
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17 |
Merge Columns |
together |
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2 |
Merge(final) |
Output final reports |
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1 |
Merge_SNPs_/_InDels_data_files |
Merge SNPs / InDels data files |
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1 |
MergeBamAlignment |
merge alignment data with additional info stored in an unmapped BAM dataset |
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11 |
MergeBED |
combine overlapping/nearby intervals into a single interval |
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17 |
MergeSamFiles |
merges multiple SAM/BAM datasets into one |
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11 |
MetaGeneAnotator |
find ORFs |
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1 |
MOL to CML |
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2 |
MOL to MOL2 |
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2 |
MOL to SMILES |
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2 |
MOL2 to CML |
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2 |
MOL2 to InChI |
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2 |
MOL2 to MOL |
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2 |
MOL2 to SDF |
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2 |
MOL2 to SMILES |
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2 |
MultiCovBed |
counts coverage from multiple BAMs at specific intervals |
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17 |
Multiple Intersect |
identifies common intervals among multiple interval files |
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21 |
NormalizeFasta |
normalize fasta datasets |
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11 |
NucBed |
profile the nucleotide content of intervals in a FASTA file |
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17 |
OverlapBed |
computes the amount of overlap from two intervals |
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17 |
Paste |
two files side by side |
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1 |
PhixRemove |
Remove phiX174 |
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1 |
Qual_Filter_FASTQFASTA |
Quality filter |
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1 |
QualityScoreDistribution |
chart quality score distribution |
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11 |
RandomBed |
generate random intervals in a genome |
|
18 |
RefSeq Search |
Similarity Search |
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1 |
ReldistBed |
calculate the distribution of relative distances |
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17 |
Remove beginning |
of a file |
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1 |
ReorderSam |
reorder reads to match ordering in reference sequences |
|
14 |
ReplaceSamHeader |
replace header in a SAM/BAM dataset |
|
14 |
Report(interim) |
Output interim reports |
|
1 |
Reverse Complement |
a MAF file |
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1 |
RevertOriginalBaseQualitiesAndAddMateCigar |
revert the original base qualities and add the mate cigar tag |
|
11 |
RevertSam |
revert SAM/BAM datasets to a previous state |
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11 |
RNAmmer 1.2 |
find rRNAs |
|
1 |
RSEM calculate expression |
RNA-Seq by Expectation-Maximization |
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1 |
RSEM prepare reference |
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1 |
RSEM trinity fasta to gene map |
extract transcript to gene map from trinity |
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2 |
Sailfish |
transcript quantification from RNA-seq data |
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1 |
SAM-to-BAM |
convert SAM to BAM |
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11 |
SamToFastq |
extract reads and qualities from SAM/BAM dataset and convert to fastq |
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14 |
SDF to CML |
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2 |
SDF to InChI |
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2 |
SDF to mol2 |
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2 |
SDF to SMILES |
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2 |
Secure Hash / Message Digest |
on a dataset |
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1 |
sed |
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1 |
Select |
lines that match an expression |
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1 |
Select first |
lines from a dataset |
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1 |
Select last |
lines from a dataset |
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1 |
Select random lines |
from a file |
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2 |
SFF converter |
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1 |
ShuffleBed |
randomly redistrubute intervals in a genome |
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18 |
SICER |
Statistical approach for the Identification of ChIP-Enriched Regions |
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2 |
SlopBed |
adjust the size of intervals |
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18 |
SMILES to CML |
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2 |
SMILES to InChI |
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2 |
SMILES to MOL |
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2 |
SMILES to MOL2 |
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2 |
SMILES to SDF |
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2 |
SMILES to SMILES |
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2 |
SnpEff |
Variant effect and annotation |
|
1 |
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 |
Split MAF blocks |
by Species |
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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 |
|
17 |
Summary Statistics |
for any numerical column |
|
3 |
Tabular to CSV |
converter |
|
1 |
TagBed |
tag BAM alignments based on overlaps with interval files |
|
17 |
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 |
|
11 |
VCF to MAF Custom Track |
for display at UCSC |
|
1 |
Visualize distribution of DNA polymorphism |
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1 |
Wig/BedGraph-to-bigWig |
converter |
|
2 |
Wiggle to Interval |
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1 |
Wiggle-to-Interval |
converter |
|
1 |
WindowBed |
find overlapping intervals within a window around an interval |
|
17 |