Code

Publicly available code is available from my GitHub repositories page.

• Among these code repositories, entrez_qiime is a utility to generate an id-to-taxonomy mapping file for taxonomy assignment using BLAST in QIIME 1. It proved particularly useful for generating mapping files for non-standard organisms and genetic markers – i.e. those for which good databases were not already available. QIIME 1 has since been succeeded by QIIME 2, and the range of taxonomic resources has expanded greatly. The entrez_qiime utility remains available mainly for reproducibility of old analyses, or in case the code can be repurposed.

For code from CRREL, please visit my ERDC GitLab page (ERDC access only).