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Bactopia Documentation

website·Indexed 32 days ago

https://bactopia.io

A Nextflow-based workflow for processing Nanopore and Illumina sequencing data for bacterial genomes, featuring tools for antimicrobial resistance screening, CLI commands, subworkflows, and modules.

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What's inside Bactopia

  1. Overview of Bactopia bacterial genome analysis workflow

    Bactopia is an end-to-end Nextflow pipeline designed to process Nanopore and Illumina sequencing data for the analysis of bacterial genomes. It provides a comprehensive workflow for genomic characterization, from raw sequencing data to final analysis results.

  2. Remove human reads from sequencing data

    Human contamination can be removed from sequencing data using the nohuman subworkflow (which utilizes the nohuman_download and nohuman_run modules). For SRA submission specifically, the srahumanscrubber subworkflow is available, utilizing srahumanscrubber_initdb and srahumanscrubber_scrub.

  3. Perform variant calling and SNP alignment with Snippy

    Bactopia uses Snippy for haploid variant calling against a reference genome via the snippy_run subworkflow/module. Core-genome SNP alignments can then be generated using the snippy_core subworkflow/module, and pairwise SNP distances calculated via the snpdists subworkflow/module.

  4. Predict phenotypic traits from microbial genomes using Traitar

    Bactopia provides the traitar subworkflow to predict phenotypic traits. This involves two main components:

    • traitar_download: Downloads the required Pfam database.
    • traitar_run: Executes the phenotypic trait prediction from microbial genomes.

  5. Identify and serotype Shiga toxin-producing E. coli with stecfinder and stxtyper

    Bactopia includes tools for Shiga toxin-producing E. coli analysis:

    • stecfinder: Used to identify and determine the serotype of Shiga toxin-producing E. coli.
    • stxtyper: Used to identify and type Stx operons from assembled genomic sequences.

  7. Functional Annotation and Protein Search

    Bactopia enables functional annotation of proteins and searching protein databases.

    Available tools:

    • eggNOG-mapper: Functional annotation through orthology assignment
    • BLASTX: Translate nucleotide sequences and search protein databases

  10. Predict serotypes for specific bacterial species

    Bactopia provides specialized serotyping tools:

    • Salmonella: seqsero2 (assemblies), sistr (assemblies/CLI).
    • Streptococcus pneumoniae: seroba (k-mer based), pneumocat (Illumina reads).
    • Shigella/EIEC: shigapass, shigatyper (reads/assemblies), shigeifinder (assemblies).
    • Pseudomonas aeruginosa: pasty (assemblies).
    • Staphylococcus aureus: spatyper (spa types), sccmec (SCCmec elements).
    • Neisseria gonorrhoeae: ngmaster (MAST/Serotyping).