BioBits blog

Rapid and Reproducible RSSC Sequevar Typing with Snakemake

A Snakemake pipeline for automated Ralstonia solanacearum species complex (RSSC) sequevar typing based on the endoglucanase (egl) gene — from genome assemblies to phylogenetic tree and sequevar assignment in one command.

8 min read   ·   March 13, 2026

2026   ·   ralstonia   rssc   sequevar   phylogenetics   snakemake   iqtree2   mafft   bacterial-genomics   reproducible-research   workflow-management   ·   bioinformatics   plant-pathology   snakemake

Superior Bacterial Genome Assembly with Autocycler Consensus and Snakemake

A comprehensive Snakemake pipeline that leverages Autocycler consensus assembly to achieve superior quality bacterial genomes from Oxford Nanopore sequencing data

10 min read   ·   September 22, 2025

2025   ·   oxford-nanopore   autocycler   bacterial-genomics   consensus-assembly   reproducible-research   workflow-management   ·   bioinformatics   genomics   nanopore   snakemake

Adventures in Bacterial Genome Assembly with Snakemake

2 min read   ·   September 17, 2025

2025   ·   assembly   bioinformatics   genomics   ·   bioinformatics   snakemake   gitlab

Introducing the qPCR Primer Analyzer ILVO

2 min read   ·   August 20, 2025

2025   ·   qPCR   in-silico   html   bioinformatics   genomics   ·   bioinformatics   genomics   tools

Batch In-Silico (q)PCR Made Easy with run_epcr.py

3 min read   ·   August 06, 2025

2025   ·   PCR   in-silico   python   bioinformatics   genomics   ·   bioinformatics   genomics   tools