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Description Short read alignment tools.
Component Version Inputs Outputs Description
Align 1.0 reads, mates, reference out

This component aligns sequencing reads to the reference genome using the Borrows-Wheeler aligner with the mem algorithm.

Complete documentation:

BamCombiner 2.0 in out

Merges multiple bam files using the Picard MergeSamFiles.

BamReducer 1.0 reference, bam alignment

This function reduces the reads in a bam file using the Genome Analysis Toolkit (GATK) 2 and outputs a dramatically more compressed bam file.

BamRegrouper 1.0 bam alignment

Picard-tools is used to add or replace read group information for each read in the input alignment file.

BamReorder 1.0 reference, bam alignment This function reorders reads in a BAM file to match the contig ordering in the provided reference file. .
BamStats 1.0 bam, refGenome, targets, chrLength, markStats report, summary The function collects alignment and coverage statistics from a bam file.
BaseRecalibrator 1.0 reference, bam, dbsnp, mask, intervals alignment, report, plots

This function will do base quality score recalibration using Genome Analysis Toolkit (GATK).

BismarkAlign 1.0 reads, refGenome, mates methylationCalls, bedGraph, alignment, Mbias, report, analysis Performs alignment of bisulfite sequencing data in addition to deduplication and methylation extraction using Bismark Bisulfite Mapper.
Blast 1.0 query, dbSeq result Basic local alignment search tool.
BSAlign 1.0 reference, reads, mates alignedReads Aligns BS or RRBS data though BSMAP software, version 2.74.
DuplicateMarker 2.0 in outBam, outMetrics

Mark PCR and optical duplicate reads in BAM files using Picard MarkDuplicates.

FusionCaller 1.0 reads, mates out Gene fusion detection.
FusionVisualizer 1.1 fusionList, annotations, reads, mates folder Post-processing tool for fusion transcripts visualization.
PrepRnaBam 1.0 reference, in, dbsnp, mask alignment, markReport, recalReport Preprocessing of RNA bam files according to GATK best practices (adding groups, marking duplicates, splitNtrim and base recalibration).
Realigner 1.0 reference, bam1, bam2, knownTargets, indels1, indels2, indels3, intervals realignedCase, realignedControl, targets

This function will do local realignment around indels using Genome Analysis Toolkit (GATK).

Complete documentation:

ReferenceIndexer 1.0 reference index The following auxiliary files for the reference fasta sequence will be created:
  • 1.
Sam2Fastq 1.0 alignment folder, reads, mate This function uses the Picard java library to perform a conversion from SAM/BAM alignment format back to FASTQ sequence format.
SelectMethContext 1.0 methCall cpg, chg, chh, statistics Separate cytosines based on the methylation context in which they occur and produces statistics about context methylation.
STAR 2.0 genome, reads, mates, parameters folder, alignment, spliceJunctions Spliced Transcripts Alignment to a Reference for RNA-seq The reason to implement STAR component was that TopHat is around 50 times slower, and that time is counted in days.
Star2Pass 1.0 reference, reads, mates, genome, annotation, parameterFile, custom folder, alignments, spliceJunctions Runs STAR aligner in two pass mode for an array of samples together.
STARGenome 0.1 genomeFasta, annotation, spliceJunctions genome Spliced Transcripts Alignment to a Reference for RNA-seq See the STAR component for more documentation.

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