. Author manuscript; available in PMC: 2018 Mar 20.

Published in final edited form as: IEEE Trans Biomed Eng. 2016 Oct 10;64(2):263–273. doi: 10.1109/TBME.2016.2573285

TABLE IV.

Selected Tools for -Omic Data Pre-processing

Tool	Assay	-Omic Data	Key Functionality
GMAP^* [63]	Next- generatio n sequenci ng	Genomic, transcriptomic , and epigenomic	Sequence mapping
BWA^* [64]
STAR^* [65]
GATK^* [30]		Genomic	Genomic variant discovery
SAMtools^* [66]		Genomic	Genomic variant discovery
HTSeq^* [67]		Transcriptomi c	Gene and transcript expression quantification
BEDTools^* [68]			Gene and transcript expression quantification
RSEM^* [69]			Gene and transcript expression quantification
Cufflinks^* [70]			Gene and transcript expression quantification
defuse [25]			Gene fusion detection
TopHat-Fusion [24]			Gene fusion detection
Trans-ABySS^* [71]			Alternative splicing detection and quantification
Trinity^* [72]
Cufflinks^* [70]
Scripture^* [73]
MACS^* [74]		Epigenomic	ChIP-seq peak calling
SISSRs^* [75]		Epigenomic	ChIP-seq peak calling
OpenMS [76]	Mass spectrom etry	Proteomic and metabolomic	Peak detection and quantification
MZmine 2^* [77]	Mass spectrom etry	Proteomic and metabolomic	Peak detection and quantification

GMAP stands for genomic mapping and alignment program; BWA, Burrows-Wheeler aligner; STAR, spliced transcripts alignment to a reference; GATK, genome analysis toolkit; RSEM, RNA-seq by expectation-maximization; Trans-ABySS, transcriptome assembly and analysis pipeline; MACS, model-based analysis of ChIP-seq; and SISSRs, site identification from short sequence reads.

Highly impactful tool with more than 50 citations per year.