spoligotyper

In silico spoligotyping of Mycobacterium tuberculosis complex (MTBC) samples, from sequencing reads (fastq) or genome assemblies (fasta). spoligotyper 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.

Sample     SpacerCount           Binary                                       Octal            Hexadecimal        Spoligotype
AF2122_97  56:47:0:58:63:0:...   1101101000001110111111111111111111111100000  664073777777600  6D-03-5F-7F-FF-60  SB0140

Features

• Reads or assemblies: single-end or paired-end fastq, or fasta, gzipped or not. Illumina and nanopore reads.
• Fast: a few seconds per sample, with 1 GB of memory.
• All the standard codes: binary, octal, hexadecimal, and SB number for M. bovis and other animal-adapted lineages.
• Transparent: the number of reads supporting each spacer is reported, and borderline calls are flagged.

Installation

conda install -c conda-forge -c bioconda spoligotyper

Or with pip, if BBTools is already installed (conda install -c bioconda bbmap): pip install spoligotyper. See Installation for other options.

Quick start

spoligotyper -r1 sample_R1.fastq.gz -r2 sample_R2.fastq.gz -o results/   # Paired-end reads
spoligotyper -r1 sample.fastq.gz -o results/                             # Single-end or nanopore reads
spoligotyper -r1 assembly.fasta -o results/                              # Assembly

The report is printed and saved as results/<sample>_spoligotyping.txt. New to the tool? The tutorial types three public genomes in a few minutes.

Documentation

The wiki covers usage and options, output files, how it works, troubleshooting and the FAQ.

Citing

If you use spoligotyper, please cite this repository (GitHub's "Cite this repository" button gives APA and BibTeX formats), and BBTools: Bushnell B. BBTools. https://sourceforge.net/projects/bbmap/

Contributing

Bug reports, questions and pull requests are welcome: see CONTRIBUTING.md.

Author

Marc-Olivier Duceppe, Canadian Food Inspection Agency (CFIA): marc-olivier.duceppe@inspection.gc.ca

License

MIT