MASTMAST is a Nextflow pipeline for antimicrobial resistance prediction from Mycobacterium tuberculosis single-end amplicon sequencing data. It performs read trimming, alignment to H37Rv, primer trimming, variant calling, variant filtering, comparison against resistance and lineage catalogues, and generates DOCX resistance reports plus TSV mutation outputs.Versions

v1.1.0 (default)

Tags: Mycobacterium tuberculosis, AMR prediction, amplicon sequencing, NextflowParameters

fastq (file, multiple) required: Single-end FASTQ.GZ amplicon sequencing files. Filenames should match barcode entries in patient_info.csv.

patient_info_csv (file) required: Patient_information file used by MAST for barcode matching and report customization.

Links

License: GPL-3.0

Cite as: MAST: Mycobacteria Amplicon Sequencing Tool. https://doi.org/10.5281/zenodo.19166350

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