Translational Biomedical Informatics in the Cloud: Present and Future

Table 2

Application of cloud computing in bioinformatics research.

Software	Website	Description	Reference
ArrayExpressHTS	http://www.ebi.ac.uk/Tools/rwiki/	RNA-Seq data processing and quality assessment	[76]
Bioscope	http://www.lifescopecloud.com/	Reference-based read mapping	[77]
Cloud-MAQ	http://sourceforge.net/projects/cloud-maq/	Read mapping and assembly	[78]
CloudAligner	http://sourceforge.net/projects/cloudaligner/	Read mapping	[79]
CloudBurst	http://cloudburst-bio.sourceforge.net/	Reference-based read mapping	[6]
CloudCoffee	http://www.tcoffee.org/homepage.html	Multiple sequence alignment	[20]
Contrail	http://contrail-bio.sourceforge.net/	De novo read assembly	[80]
Crossbow	http://bowtie-bio.sourceforge.net/crossbow/	Read mapping and SNP calling	[4]
FX	http://fx.gmi.ac.kr/	RNA-Seq data analysis for gene expression levels and genomic variant calling	[81]
GeneSifter	http://www.geospiza.com/Products/AnalysisEdition.shtml	Customer-oriented NGS data analysis services	[82]
Myrna	http://bowtie-bio.sf.net/myrna/	Differential expression analysis for RNA-Seq data	[83]
PeakRanger	http://www.modencode.org/software/ranger/	Peak caller for ChIP-Seq data	[84]
Roundup	http://rodeo.med.harvard.edu/tools/roundup/	Optimized computation for comparative genomics	[19]
SeqMapReduce	http://www.seqmapreduce.org/	Read mapping	[85]
YunBe	http://tinyurl.com/yunbedownload/	Gene set analysis for biomarker identification	[86]