CLOSET r78 – CLoud Open SequencE clusTering

CLOSET r78

:: DESCRIPTION

CLOSET is a map-reduce framework for clustering sequences from metagenomic samples, such as 454 reads.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • HADOOP cluster

:: DOWNLOAD

  CLOSET

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340001. doi: 10.1142/S0219720013400015. Epub 2012 Dec 25.
Large-scale metagenomic sequence clustering on map-reduce clusters.
Yang X1, Zola J, Aluru S.

GenomeVIP v1.2.1 – Cloud based Genome Variant Investigation Platform

GenomeVIP v1.2.1

:: DESCRIPTION

GenomeVIP is a web application platform for performing variant discovery on Amazon’s Web Service (AWS) cloud or on local high-performance computing clusters.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GenomeVIP

:: MORE INFORMATION

Citation

Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Feny? D, Raphael BJ, Wendl MC, Ding L.
GenomeVIP: a cloud platform for genomic variant discovery and interpretation.
Genome Res. 2017 Aug;27(8):1450-1459. doi: 10.1101/gr.211656.116. Epub 2017 May 18. PMID: 28522612; PMCID: PMC5538560.

FX 1.0.5 – RNA-Seq analysis tool on the Cloud

FX 1.0.5

:: DESCRIPTION

FX is a user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing. With FX, you can simply upload your RNA-Seq raw FASTQ data on the cloud, and let the computing infra to do the heavy analysis.

::DEVELOPER

Genomic Medicine Institute, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FX

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Mar 1;28(5):721-3. doi: 10.1093/bioinformatics/bts023. Epub 2012 Jan 17.
FX: an RNA-Seq analysis tool on the cloud.
Hong D1, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, Chong H, Yang KS, Lee YS, Kim IH, Lee JS, Kim JI, Seo JS.

SIMPLEX 2.0 – Cloud-enabled pipeline for the comprehensive analysis of Exome Sequencing data

SIMPLEX 2.0

:: DESCRIPTION

SIMPLEX is a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow. The pipeline combines several in-house developed and published applications to perform the following steps: (a) initial quality control, (b) intelligent data filtering and pre-processing, (c) sequence alignment to a reference genome, (d) SNP and DIP detection, (e) functional annotation of variants using different approaches, and (f) detailed report generation during various stages of the workflow.

::DEVELOPER

the Division of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

:: DOWNLOAD

 SIMPLEX

 :: MORE INFORMATION

Citation

SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, Zschocke J, Trajanoski Z, Stocker G.
PLoS One. 2012;7(8):e41948. doi: 10.1371/journal.pone.0041948.