This repository contains scripts and manuals for whole genome sequencing based analysis of non-tuberculous mycobacteria. Questions? Ask [email protected]

The wrapper script starter_NTMseq.sh runs on linux and accepts FastQ (illumina) and FastA files as input. It includes:

1. Quality control of raw sequence reads [Input: FastQ files; Required tools: FastQC and multiQC]
2. Contamination detection [Input: FastQ files or FastA files; Required tools: kraken2]
3. Preprocessing of raw sequence reads (e.g. adapter removal) [Required tools: fastp]
4. Mycobacterium (sub)species and resistance prediction [Input: FastQ files; Required tools: NTMprofiler]
5. Multi-locus sequence typing (MLST) [Input: FastQ files; Required tools: srst2; Required database: pubMLST (only available for M. abscessus)]
6. Assembly of sequence reads [Input: FastQ files; Required tools: Shovill; Output: FastA files]
7. Fast phylogenetic analysis using Mashtree [Input: FastQ files or FastA files; Required tools: Mashtree]
8. Detection of known plasmids [Input: FastQ files; Required tools: srst2 and seqkit; Required database: PLSDB or custom]
9. De novo prediction of plasmid contigs [Input: FastQ files; Required tools: platon and/or plasmidspades]
10. Resistance and virulence gene prediction [Input: FastA files; Required tools: AMRfinder+]

For complete installation instructions of NTMseq, description and usage examples please send a mail to [email protected].

Diricks et al., 2022: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01017-x --> see folder scripts/2022_Diricks_abscessus