PT  - JOURNAL ARTICLE
AU  - Michal Stolarczyk
AU  - Vincent P. Reuter
AU  - Neal E. Magee
AU  - Nathan C. Sheffield
TI  - Refgenie: a reference genome resource manager
AID  - 10.1101/698704
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 698704
4099  - http://biorxiv.org/content/early/2019/07/12/698704.short
4100  - http://biorxiv.org/content/early/2019/07/12/698704.full
AB  - Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; for example, many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this. To this end, we introduce refgenie, a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command-line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.Availability https://refgenie.databio.org