A reproducible workflow for Pacheco-Valenciana, 2026

COMING SOON 👩🏻‍💻

A reproducible bioinformatics workflow we implemented to investigate the population genetics and evolutionary forces acting on the prevalent, vitamin-B-provisioning Baltic Sea archaeon described by Armando Pacheco-Valenciana et al in the study titled “A streamlined and abundant Nitrosopumilus population retains vitamin biosynthesis under high purifying selection in the Baltic Sea” will be here soon. On this page we will detail how we started with anvi-split to obtain anvi’o artifacts for a single MAG and proceeded to (1) identify metagenomes in which the genome is confidently covered, (2) resolve population structure across samples through single-nucleotide variants and Fst, revealing a clustering that tracks both environmental parameters and biogeography, (3) test whether the genes involved in vitamin B (B1, B7, B12) biosynthesis are under stronger purifying selection than the genomic background via a per-gene pN/pS analysis, and (4) place the presence/absence of these biosynthetic genes in the broader context of the ammonia-oxidizing archaeal tree using GlobDB.

Everything is there, and we just need a bit more time to make it as polished as needed for your eyes. Thank you for your understanding.