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spoligotyper performs in silico spoligotyping of Mycobacterium tuberculosis complex (MTBC) samples from sequencing reads (fastq) or genome assemblies (fasta). It finds the 43 spacers of the direct repeat (DR) locus with Seal from BBTools, and reports the spoligotype as binary, octal and hexadecimal codes, and as an SB number from the Mbovis.org database.
It also identifies the species (regions of difference RD1, RD4, RD7, RD9, RD12) and the lineage (SNP barcode), estimates how much of the sample is MTBC, and flags mixed or contaminated samples.
It types one sample or a whole folder of samples (fastq and fasta files are detected and R1/R2 files paired automatically), and writes a table and a PDF report with everything needed for quality assurance: the evidence for each call, input files and checksums, software versions, parameters, operator and date.
It works for all members of the complex (M. tuberculosis, M. bovis, M. caprae, M. pinnipedii, M. microti, M. africanum, M. canettii, ...). SB numbers are only defined for the animal-adapted lineages (RD9-deleted: M. bovis, M. caprae, ...); for human-adapted lineages, use the octal code (see the FAQ).
- Installation
- Tutorial: three public genomes, step by step
- Usage: input files, options and examples
- Output files: the table, column by column, and the PDF report
- How it works: spoligotyping, spacer detection, and the choice of the minimum count
- Species and lineage: species check, lineage, contamination and mixed samples
- Validation: reference genomes and read sets of known species, lineage and spoligotype
Please cite spoligotyper: Duceppe M-O. spoligotyper: in silico spoligotyping of Mycobacterium tuberculosis complex genomes. Zenodo. https://doi.org/10.5281/zenodo.22926160 (all versions; each release also has its own DOI on Zenodo). Please also cite BBTools: Bushnell B. BBTools. https://sourceforge.net/projects/bbmap/