title: Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab.
abstract: The khmer software project provides both research and production functionality for largescale nucleic-acid sequence analysis. The software implements several novel data structures and algorithms that perform data pre-fltering for common bioinformatics tasks, including sequence mapping andde novoassembly. Development is driven by a small lab with one full-time developer (MRC), as well as several graduate students and a professor (CTB) who contribute regularly to research features. Here we describe our efforts to bring better design, testing, and more open development to the khmer software project as of version 1.1. The khmer software is developed openly at http://github.com/dib-lab/khmer/.
authors.affiliation: Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Crusoe
authors.affiliation: Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
authors.forename: C Titus
authors.initials: CT
authors.lastname: Brown
keywords: WSSSPE; k-mer