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Special Issues
BioMed Research International
/
2013
/
Article
/
Tab 1
/
Review Article
Enabling Large-Scale Biomedical Analysis in the Cloud
Table 1
Cloud-based bioinformatics tools.
Program
Description
URL
Reference
Sequence alignment
Cloud-Coffee
Multiple sequence alignment
http://www.tcoffee.org/
[
15
]
USM
MapReduce solution to sequence comparison
http://usm.github.io/
[
16
]
Sequence mapping and assembly
CloudBurst
Reference-based read mapping
http://cloudburst-bio.sourceforge.net/
[
17
]
CloudAligner
Short read mapping
http://cloudaligner.sourceforge.net/
[
18
]
SEAL
Short read mapping and duplicate removal
http://biodoop-seal.sourceforge.net/
[
19
]
Crossbow
Combine sequence aligner Bowtie and the SNP caller SOAPsnp [
20
]
http://bowtie-bio.sourceforge.net/crossbow/
[
21
]
Contrail
De novo
assembly
http://contrail-bio.sourceforge.net/
[
22
]
Eoulsan
Sequencing data analysis
http://transcriptome.ens.fr/eoulsan/
[
23
]
Quake
Quality-aware detection and correction of sequencing errors
http://www.cbcb.umd.edu/software/quake/
[
24
]
Gene expression
Myrna
Differential expression analysis for RNA-seq
http://bowtie-bio.sourceforge.net/myrna/
[
25
]
FX
RNA-seq analysis tool
http://fx.gmi.ac.kr/
[
26
]
ArrayExpressHTS
RNA-seq process and quality assessment
http://www.ebi.ac.uk/services
[
27
]
Comprehensive application
BioVLab
A virtual collaborative lab for biomedical applications
https://sites.google.com/site/biovlab/
[
28
]
Hadoop-BAM
Directly manipulate NGS data
http://sourceforge.net/projects/hadoop-bam/
[
29
]
SeqWare
A scalable NoSQL database for NGS data
http://seqware.sourceforge.net
[
30
]
PeakRanger
Peak caller for ChIP-seq data
http://ranger.sourceforge.net/
[
31
]
YunBe
Gene set analysis for biomarker identification
http://tinyurl.com/yunbedownload/
[
32
]
GATK
Genome analysis toolkit
http://www.broadinstitute.org/gatk/
[
33
]
Cloud BioLinux
A virtual machine with over 135 bioinformatics packages
http://cloudbiolinux.org/
[
34
]
CloVR
A virtual machine for automated sequence analysis
http://clovr.org/
[
35
]