Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next-Generation Sequencing Era

Table 3

The cloud computing software for NGS data analysis.

Software	Website	Description	References
Crossbow	http://bowtie-bio.sourceforge.net/crossbow/	Read mapping and SNP calling	[56]
CloudBurst	http://cloudburst-bio.sourceforge.net/	Reference-based read mapping	[57]
Contrail	http://contrail-bio.sourceforge.net/	De novo read assembly	[58]
Cloud-MAQ	http://sourceforge.net/projects/cloud-maq/	Read mapping and assembly	[59]
Bioscope	http://www.lifescopecloud.com/	Reference-based read mapping	[60]
GeneSifter	http://www.geospiza.com/Products/AnalysisEdition.shtml	Customer oriented NGS data analysis services	[61]
CloudAligner	http://sourceforge.net/projects/cloudaligner/	Read mapping	[62]
Roundup	http://rodeo.med.harvard.edu/tools/roundup	Optimized computation for comparative genomics	[63]
PeakRanger	http://www.modencode.org/software/ranger/	Peak caller for ChIP-Seq data	[64]
Myrna	http://bowtie-bio.sf.net/myrna/	Differential expression analysis for RNA-Seq data	[65]
ArrayExpressHTS	http://www.ebi.ac.uk/Tools/rwiki/	RNA-Seq data processing and quality assessment	[66]
SeqMapreduce	Not available	Read mapping	[67]
BaseSpace	https://basespace.illumina.com/home/index