Sequence database versioning for command line and Galaxy bioinformatics servers.

ABSTRACT:

Motivation

There are various reasons for rerunning bioinformatics tools and pipelines on sequencing data, including reproducing a past result, validation of a new tool or workflow using a known dataset, or tracking the impact of database changes. For identical results to be achieved, regularly updated reference sequence databases must be versioned and archived. Database administrators have tried to fill the requirements by supplying users with one-off versions of databases, but these are time consuming to set up and are inconsistent across resources. Disk storage and data backup performance has also discouraged maintaining multiple versions of databases since databases such as NCBI nr can consume 50 Gb or more disk space per version, with growth rates that parallel Moore's law.

SUBMITTER: Dooley DM 

PROVIDER: S-EPMC4824126 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature