bifidotyper 0.1.1

A bioinformatics tool for analyzing Bifidobacteria in sequencing data.

Bifidotyper

Bifidotyper is a fast, lightweight bioinformatics tool designed to take you from raw FastQ files to a complete and reproducible analysis of Bifidobacterial strains in your samples. It makes use of Sylph for rapid, k-mer-based read alignments. It also uses Salmon to detect the presence of genes necessary for the metabolism of human milk oligosaccharides (HMOs) based on alignments to the Bifidobacterium longum^1 genome using gene annotations from Henrick et al.[^2]

[^2]: Henrick, B. M. et al. (2021). Bifidobacteria-mediated immune system imprinting early in life. Cell, 184(15). https://doi.org/10.1016/j.cell.2021.05.030

Bifidotyper was developed as part of a PhD rotation in the Olm Lab and the IQ Biology program.

Installation

Bifidotyper can be installed with pip but it depends on Sylph and Salmon, which don't have pip distributions. You can install both with Conda (conda install -c bioconda sylph salmon), but for ease of use, binaries are included for Sylph and automatically downloaded for Salmon if they aren't found in your PATH.

Clone the repository and install the package:

git clone https://github.com/Bennibraun/bifidotyper.git
cd bifidotyper
pip install -e .

A proper distribution via PyPI or Anaconda is planned.

Usage

Command Line Interface

For single-end reads:

bifidotyper -se <single-end FASTQ files> [-t <threads>] [-g <genome-dir> | -s <genome-sketch>]

Or paired-end reads:

bifidotyper -pe <paired-end FASTQ files> [--r1-suffix <R1 suffix>] [--r2-suffix <R2 suffix>] [-t <threads>] [-g <genome-dir> | -s <genome-sketch>]

Options

• -se, --single-end: Single-end FASTQ files.
• -pe, --paired-end: Paired-end FASTQ files (R1 and R2 files, supports wildcards).
• -t, --threads: Number of threads to use for parallel processing (default: 1).
• --r1-suffix: Suffix for R1 files (optional, only for paired-end mode. Default: "_R1").
• --r2-suffix: Suffix for R2 files (optional, only for paired-end mode. Default: "_R2").
• -g, --genome-dir: Directory containing reference genomes (optional, defaults to provided genomes).
• -s, --genome-sketch: Path to a pre-sketched Sylph genome database (optional, defaults to provided database). Use sylph sketch *.fna to generate your own database.

Examples

# Run bifidotyper in paired-end mode with 4 threads and _R1/_R2 suffixes
bifidotyper -pe data/*.fastq.gz --r1-suffix _R1 --r2-suffix _R2 -t 4
# Run bifidotyper in single-end mode with 8 threads and a custom genome directory
bifidotyper -se data/*.fastq.gz -t 8 -g my_genomes/

Output

The tool generates several output files and directories:

• plots/: All plots generated by the program.
• sylph_genome_sketches/: The database of Sylph genome indices.
• sylph_fastq_sketches/: K-mer indices of input samples processed with Sylph.
• sylph_genome_queries/: Results of running Sylph queries against the genomes.
• hmo_quantification/: HMO gene alignments with Salmon.

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Provided Reference Files

• HMO functional annotations were retrieved from Henrick et al. 2021. The table is provided in src/data/reference/humann2_HMO_annotation.csv
• All B. longum annotations are from the NCBI record for CP001095.1
• A pre-processed Sylph genome database is provided for ease of use. Any genome matching the family Bifidobacterium in NCBI and GTDB was included. The genome database was dereplicated with dRep with --S_ani 0.95 before indexing. All genome accessions are listed in src/data/reference/genomes.csv

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License

This project is licensed under the MIT License.

Contributing

Contributions are welcome! Please open an issue or submit a pull request on GitHub.