brucellaid 1.0.0

Identify the Brucella species of a fastq sample by its MASH distance to 16 reference genomes, and type it with the nine-locus Whatmore MLST scheme, whose alleles are called from the reads with Seal from BBTools. Point it at a sample, or a folder of samples.

$ brucellaid -r1 sample_R1.fastq.gz -r2 sample_R2.fastq.gz -o results/
Sample  Species           Biovar  ClosestReference           MashDistance  SharedHashes  SequenceType  AlleleProfile
sample  Brucella abortus  1       NC_006932-NC_006933.fasta  0.000024      999/1000      1             2-1-1-2-1-3-1-1-1

Both the reference sketch and the MLST database come with the package: nothing to download, index or configure.

Features

• Two independent answers: the species, from the closest of 16 Brucella reference genomes, and the sequence type, from the nine MLST alleles. Neither call corrects the other, and both come with the numbers they rest on.
• Nothing is hidden: the distance to every reference, the reads behind every allele call and the runner-up that call had to beat, a note when a second reference was nearly as close, and a tie reported as a tie rather than broken by a coin toss.
• Batch mode: point it at a folder; fastq files are found recursively, R1/R2 paired, and several samples run at a time. A sample that fails leaves the others readable.
• Current reference data: the MLST database is PubMLST's, 309 alleles and 122 sequence types, rebuilt by a script in the repository. The sketch is vSNP's 16 Brucella genomes, with the species, biovar, strain and accession of each.
• Backwards compatible where it counts: the species identification is vSNP's, down to the threshold of 150 shared hashes, and --xlsx still writes the stat_alignment_summary_<date>.xlsx of the first version.
• Nothing to configure: only the Python standard library, plus MASH and BBTools.
• Tested: 194 tests, 100% coverage, end to end on a synthetic genome and on reads tiled over the real MLST alleles.
• Validated on 16 genomes with a known answer: every species, biovar and closest reference right, and all 14 sequence types the one the genome carries — read off the assembly by exact match, which shares no code with the read-based caller. The nearest neighbouring species shares 4 of 1000 hashes and comes back as not identified (Validation).

Installation

conda create -n brucellaid -c conda-forge -c bioconda brucellaid
conda activate brucellaid

MASH and BBTools (which provides seal.sh) are not on PyPI, so they come from bioconda; BrucellaID itself needs nothing else. See Installation for pip and for running it from a clone.

Quick start

brucellaid -r1 sample_R1.fastq.gz -r2 sample_R2.fastq.gz -o results/  # Paired-end reads
brucellaid -r1 sample.fastq.gz -o results/                            # Single-end reads
brucellaid -i reads/ -o results/ -p 4                                 # A folder, 4 samples at a time
brucellaid -i reads/ -o results/ --no-mlst                            # Species only

The results are printed and saved in results/: one row per sample, one row per locus, every MASH distance, and a JSON report. To see it work on data with a known answer, run bash examples/run_example.sh, which builds its own reads from the alleles of a sequence type.

What the two answers mean: the species is the species of the closest reference genome, and the biovar is that reference's biovar, which is not the same as a biovar call — the Brucella biovar references differ by very little. The sequence type is new when the nine alleles are called but the combination is not in the table, and ND when a locus could not be called. See How it works.

Documentation

The wiki covers installation, a tutorial on public read sets, usage and options, output files, how it works, validation, troubleshooting and the FAQ.

Citing

If you use BrucellaID, please cite it together with the tools and the data it rests on:

Duceppe M-O. BrucellaID: Brucella species identification and MLST from sequencing reads. https://github.com/duceppemo/BrucellaID

Ondov BD, Treangen TJ, Melsted P, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology 2016;17:132. https://doi.org/10.1186/s13059-016-0997-x

Bushnell B. BBTools. https://sourceforge.net/projects/bbmap/

Whatmore AM, Perrett LL, MacMillan AP. Characterisation of the genetic diversity of Brucella by multilocus sequencing. BMC Microbiology 2007;7:34. https://doi.org/10.1186/1471-2180-7-34

Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Research 2018;3:124. https://doi.org/10.12688/wellcomeopenres.14826.1

GitHub's "Cite this repository" button gives the citation in APA and BibTeX formats, from CITATION.cff.

Related

• brucetyper — in silico Bruce-ladder, Suis-ladder, AMOS and RB51 junction PCR for Brucella, from assemblies. Where BrucellaID gives the species from a distance and the sequence type from the alleles, brucetyper reads the assays a laboratory would run on a gel.
• seqcounter — count the occurrences of any reference sequences in reads or assemblies.
• spoligotyper — in silico spoligotyping of the M. tuberculosis complex.

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