When we develop software packages we try to use DevOps methods. Our larger projects employ automatic testing and using continuous integration/ continuous development servers (TravisCI and CircleCI).
Our software is available on the Genomics and Bioinformatics Unit’s Github repository USDA-ARS-GBRU Github.
When we run data analysis we are committed to publishing reproducible research by documenting the computational methods we use in analyses and making the source code of those analyses publicly available. Examples of our reproducible workflows are:
|ITSxpress||ITSxpress is a stand alone CLI and a QIIME 2 package for trimming the internally transcribed spacer regions with quality scores in amplicon sequencing experiments. The software was published in 2018 doi:10.12688/f1000research.15704.1||ITSxpress on Github and Q2-ITSxpress|
|Guidemaker||Software to globally design guide RNAs for CRISPR-Cas experiments in any organism with any Cas enzyme||Guidemaker|
Software projects prior to USDA
|Reftree||Software for querying and processing taxonomically structured data.||link|
|iTagger||Software for processing amplicon sequencing data at a scale of 10,000 samples per year.||link|
|Fidoplankter||An online calculator for designing iron limitation experiments in Phytoplankton, written before I knew about Github :)||link|