DRAW+SneakPeek: analysis workflow and quality metric management for DNA-seq experiments.

TitleDRAW+SneakPeek: analysis workflow and quality metric management for DNA-seq experiments.
Publication TypeJournal Article
Year of Publication2013
AuthorsLin C-F, Otto Valladares, D Childress M, Klevak E, Geller ET, Hwang, ii Y-C, Tsai EA, Gerard D Schellenberg, San Wang L-
JournalBioinformatics
Volume29
Issue19
Pagination2498-500
Date Published2013 Oct 1
ISSN1367-4811
KeywordsBiometry, DNA, Internet, Programming Languages, Sequence Analysis, DNA, Software Design
Abstract

SUMMARY: We report our new DRAW+SneakPeek software for DNA-seq analysis. DNA resequencing analysis workflow (DRAW) automates the workflow of processing raw sequence reads including quality control, read alignment and variant calling on high-performance computing facilities such as Amazon elastic compute cloud. SneakPeek provides an effective interface for reviewing dozens of quality metrics reported by DRAW, so users can assess the quality of data and diagnose problems in their sequencing procedures. Both DRAW and SneakPeek are freely available under the MIT license, and are available as Amazon machine images to be used directly on Amazon cloud with minimal installation.

AVAILABILITY: DRAW+SneakPeek is released under the MIT license and is available for academic and nonprofit use for free. The information about source code, Amazon machine images and instructions on how to install and run DRAW+SneakPeek locally and on Amazon elastic compute cloud is available at the National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (http://www.niagads.org/) and Wang lab Web site (http://wanglab.pcbi.upenn.edu/).

DOI10.1093/bioinformatics/btt422
Alternate JournalBioinformatics
PubMed ID23943636
PubMed Central IDPMC3777113
Grant ListP01 AG017586 / AG / NIA NIH HHS / United States
P01 AG017586 / AG / NIA NIH HHS / United States
P30 AG010124 / AG / NIA NIH HHS / United States
P30 AG010124 / AG / NIA NIH HHS / United States
P50 NS053488 / NS / NINDS NIH HHS / United States
P50 NS053488 / NS / NINDS NIH HHS / United States
R01 MH089004 / MH / NIMH NIH HHS / United States
R01 MH089004 / MH / NIMH NIH HHS / United States
R01 MH094382 / MH / NIMH NIH HHS / United States
R01 MH094382 / MH / NIMH NIH HHS / United States
U01 AG032984 / AG / NIA NIH HHS / United States
U01 AG032984 / AG / NIA NIH HHS / United States
U24 AG021886 / AG / NIA NIH HHS / United States
U24 AG041689 / AG / NIA NIH HHS / United States
U24 AG041689 / AG / NIA NIH HHS / United States