Spriggan: A Nextflow pipeline for bacterial whole genome sequence assembly and antibiotic resistance gene detection
Authors/Creators
- 1. Wisconsin State Laboratory of Hygiene
Description
Spriggan is a Nextflow pipeline for the assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes. The pipeline performs read trimming and quality assessment using BBtools and FastQC, genome assembly using Shovill, assembly quality assessment with QUAST, genome coverage calculation using BWA and Samtools, antimicrobial resistance gene detection using AMRFinderPlus, MLST scheme classification, contamination detection using Kraken2, and generates comprehensive summary reports using MultiQC.
Notes
This release does the following:
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Replaces text-based matching between Genus species (from the Kraken summary file) and the Species field in the assembly statistics database with a taxonomic ID–based approach. The workflow now:
- Parses the Kraken output file to determine the predicted tax ID (highest-percentage S rank hit).
- Matches this predicted tax ID to the Consensus_TAXID in the assembly statistics database.
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Eliminates the user-provided "taxonomy to compare" functionality for assembly statistics calculations. Taxonomic comparison is now fully based on Kraken-derived tax IDs.
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Updates workflow logic to properly handle rejected samples when running in AWS HealthOmics environment.
Files
wslh-bio/spriggan-1.8.0.zip
Files
(471.2 MB)
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Additional details
Related works
- Is supplement to
- Software: https://github.com/wslh-bio/spriggan/tree/1.8.0 (URL)
Software
- Repository URL
- https://github.com/wslh-bio/spriggan