Table 1: Cloud-based bioinformatics tools.

ProgramDescriptionURLReference

Sequence alignment
Cloud-CoffeeMultiple sequence alignmenthttp://www.tcoffee.org/[15]
USMMapReduce solution to sequence comparisonhttp://usm.github.io/[16]

Sequence mapping and assembly
CloudBurstReference-based read mappinghttp://cloudburst-bio.sourceforge.net/[17]
CloudAlignerShort read mappinghttp://cloudaligner.sourceforge.net/[18]
SEALShort read mapping and duplicate removalhttp://biodoop-seal.sourceforge.net/[19]
CrossbowCombine sequence aligner Bowtie and the SNP caller SOAPsnp [20]http://bowtie-bio.sourceforge.net/crossbow/[21]
ContrailDe novo assemblyhttp://contrail-bio.sourceforge.net/[22]
EoulsanSequencing data analysishttp://transcriptome.ens.fr/eoulsan/[23]
QuakeQuality-aware detection and correction of sequencing errorshttp://www.cbcb.umd.edu/software/quake/[24]

Gene expression
MyrnaDifferential expression analysis for RNA-seqhttp://bowtie-bio.sourceforge.net/myrna/[25]
FXRNA-seq analysis toolhttp://fx.gmi.ac.kr/[26]
ArrayExpressHTSRNA-seq process and quality assessmenthttp://www.ebi.ac.uk/services[27]

Comprehensive application
BioVLabA virtual collaborative lab for biomedical applicationshttps://sites.google.com/site/biovlab/[28]
Hadoop-BAMDirectly manipulate NGS datahttp://sourceforge.net/projects/hadoop-bam/[29]
SeqWareA scalable NoSQL database for NGS datahttp://seqware.sourceforge.net[30]
PeakRangerPeak caller for ChIP-seq datahttp://ranger.sourceforge.net/[31]
YunBeGene set analysis for biomarker identificationhttp://tinyurl.com/yunbedownload/[32]
GATKGenome analysis toolkithttp://www.broadinstitute.org/gatk/[33]
Cloud BioLinuxA virtual machine with over 135 bioinformatics packageshttp://cloudbiolinux.org/[34]
CloVRA virtual machine for automated sequence analysishttp://clovr.org/[35]