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Table 1 Cloud resources in bioinformatics

From: Bioinformatics clouds for big data manipulation

Resource

Description & availability

Data as a Service (DaaS):

AWS Public Datasets

Cloud-based archives of GenBank, Ensembl, 1000 Genomes, Model Organism Encyclopedia of DNA Elements, Unigene, Influenza Virus, etc.; http://aws.amazon.com/publicdatasets

Software as a Service (SaaS):

BGI Cloud (unpublished)

Cloud-based implementations of various genomic analysis applications; http://cloud.genomics.cn

CloudAligner [16]

Fast and full-featured MapReduce-based tool for sequence mapping; http://cloudaligner.sourceforge.net

CloudBLAST [19]

A cloud-based implementation of NCBI BLAST; http://ammatsun.acis.ufl.edu/amwiki/index.php/CloudBLAST_Project

CloudBurst [17]

Highly sensitive short read mapping with MapReduce; http://cloudburst-bio.sourceforge.net

Contrail (unpublished)

Cloud-based de novo assembly of large genomes; http://contrail-bio.sourceforge.net

Crossbow [18]

Read Mapping and SNP calling using cloud computing; http://bowtie-bio.sf.net/crossbow

EasyGenomics (unpublished)

Cloud-based NGS pipelines for whole genome resequencing, exome resequencing, RNA-Seq, small RNA and de novo assembly; http://www.easygenomics.org

eCEO [26]

Cloud-based identification of large-scale epistatic interactions in genome-wide association study (GWAS); http://www.comp.nus.edu.sg/~wangzk/eCEO.html

FX [20]

RNA-Seq analysis tool; http://fx.gmi.ac.kr

Gaea (unpublished)

Cloud-based genome re-sequencing assembly; http://bgiamericas.com/data-analysis/cloud-computing

Hecate (unpublished)

Cloud-based de novo assembly; http://bgiamericas.com/data-analysis/cloud-computing

Jnomics (unpublished)

Cloud-scale sequence analysis suite based on Apache Hadoop; http://sourceforge.net/apps/mediawiki/jnomics

Myrna [21]

Differential gene expression tool for RNA-Seq; http://bowtie-bio.sourceforge.net/myrna

PeakRanger [24]

Cloud-enabled peak caller for ChIP-seq data; http://www.modencode.org/software/ranger

RSD [23]

Reciprocal smallest distance algorithm for ortholog detection using Amazon's Elastic Computing Cloud; http://roundup.hms.harvard.edu

VAT [25]

Variant annotation tool to functionally annotate variants from multiple personal genomes at the transcript level; http://vat.gersteinlab.org

YunBe [22]

Pathway-based or gene set analysis of expression data; http://tinyurl.com/yunbedownload

Platform as a Service (PaaS):

Eoulsan [27]

Cloud-based platform for high throughput sequencing analyses; http://transcriptome.ens.fr/eoulsan

Galaxy Cloud [28, 29]

Cloud-scale Galaxy for large-scale data analysis; http://galaxy.psu.edu

Infrastructure as a Service (IaaS):

Cloud BioLinux [30]

A publicly accessible virtual machine for high performance bioinformatics computing using cloud platforms; http://cloudbiolinux.org

CloVR [31]

A portable virtual machine for automated sequence analysis using cloud computing; http://clovr.org