paper.md

title	tags	authors	date	bibliography
elvers: an automated, extensible bioinformatics workflow system	snakemake RNA-seq Python	name orcid affiliation N Tessa Pierce 0000-0002-2942-5331 University of California, Davis name orcid affiliation Charles Reid University of California, Davis name orcid affiliation C. Titus Brown 0000-0001-6001-2677 University of California, Davis	22 Mar 2019	paper.bib

Summary

elvers is a bioinformatics workflow system that leverages snakemake [@10.1093/bioinformatics/bts480] to facilitate automated and reproducible analyses.

elvers provides an extensible playbook of snakemake rules and worklows that can be mixed and matched for completely customizable automated analyses. The elvers command-line interface enables full user customization of all included programs, while handling specification of any intermediate files.

elvers requires users to input either data files (via spreadsheet), reference transcriptomes or genomes (via YAML configuration file), or both.

References