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BacFlux v2.0.0

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@iLivius iLivius released this 24 Aug 09:14
· 11 commits to main since this release
v2.0.0
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BacFlux v2.0.0 merges the four separate workflows — BacFlux, BacFluxL, BacFluxL+ and FastaFlux — into a single workflow with four entry points, and adds an optional mobilome module that asks, for every AMR gene, whether it sits in a mobile genetic element and how transferable that element is.

Full documentation: https://iLivius.github.io/BacFlux/

Breaking changes

Read these before upgrading a v1 project.

Change What to do
One repository, four modes. BacFluxL and BacFluxL+ are retired; their DOIs stay valid for published work. Set mode: in the config — illumina, nanopore, hybrid or contigs.
workflow/FastaFlux is deleted. Use mode: contigs. Same job, same config file.
Output stages renumbered. Now 01.reads, 02.assembly, 03.taxonomy, 04.annotation, 05.amr, 06.plasmids, 07.phages, 08.mobilome, 09.report. Update any downstream scripts that hard-code paths.
Rules reorganised into workflow/rules/{shared,illumina,nanopore,hybrid,contigs}/. Only matters if you patched the Snakefile.
GTDB-Tk 2.7.2 requires GTDB R232. Download R232; R226 will not work.

New

  • Mobilome module (stage 08.mobilome, 22 rules, off by default). Assigns each AMR gene one of six mobility tiers, from intrinsic_candidate to predicted_self_transmissible, with the evidence in the same row: replicon, IS context, curated element name, conjugation machinery, att sites, contig-edge flags and a confidence grade. Adds ISEScan and MacSyFinder/CONJscan. Four optional naming layers (TnCentral, ICEberg, ICEscan, ISOSDB) stay off until you supply a source.
  • geNomad as an opt-in second-opinion plasmid and virus caller. Off by default: it is licensed for academic/non-commercial use, and BacFlux is MIT. VirSorter2 remains the default.
  • Documentation site — architecture, per-stage analysis notes, method references, configuration reference and troubleshooting.
  • Point mutations surfaced via AMRFinderPlus --organism, mapped from the GTDB-Tk call. This is the intrinsic-resistance category a BLAST screen structurally cannot see.
  • Audit trails everywhere. Every filtering decision writes a TSV with a reason column, including discarded MGE predictions and refused organism mappings.

Tool versions

SPAdes 4.3.0 · Flye 2.9.6 · Medaka 2.2.2 · Polypolish 0.7.1 · dnaapler 1.4.0 · fastp 1.0.1 · QUAST 5.3.0 · CheckM 1.2.5 · GTDB-Tk 2.7.2 (GTDB R232) · Bakta 1.12.1 · eggNOG-mapper 2.1.15 · antiSMASH 8.0.4 · dbCAN 5.1.2 · ABRicate 1.4.0 · Platon 1.8 · VirSorter2 2.2.4 · CheckV 1.1.1 · geNomad 1.12.0 · ISEScan 1.7.3 · MacSyFinder 2.1.6 · MultiQC 1.33

Notes

  • Databases are never bundled. The workflow ships code and URLs; you download each database under the licensor's terms. Licence types are listed in the documentation.
  • Run it with --cores only. Do not add --jobs.
  • Citation: cite BacFlux and the tools whose output you used — see CITATIONS.md.

132 commits since v1.3.1.

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