chewcall

A high-performance allele caller for cgMLST/wgMLST schemas, inspired by and compatible with chewBBACA.

chewcall reimplements the AlleleCall algorithm from chewBBACA in Rust, replacing BLASTp with SIMD-accelerated exact Smith-Waterman protein alignment via parasail.

Installation

Requirements

• Rust 1.75+ (install via rustup)
• parasail (SIMD-accelerated Smith-Waterman library)
• Optional: CUDA 12+ and NVIDIA GPU (for --gpu mode)

Build

# Build parasail (one-time)
git clone https://github.com/jeffdaily/parasail.git
cd parasail && mkdir build && cd build
cmake .. && make -j$(nproc)
cd ../..

# Standard build
RUSTFLAGS="-C target-cpu=native" cargo build --release

# With GPU support (requires CUDA)
CUDA_HOME=/usr/local/cuda RUSTFLAGS="-C target-cpu=native" cargo build --release

# Run (parasail must be in LD_LIBRARY_PATH)
LD_LIBRARY_PATH=/path/to/parasail/build ./target/release/chewcall [OPTIONS]

The binary is at target/release/chewcall.

Usage

Quick start

# Run allele calling (built-in CDS prediction via prodigal-rs)
chewcall \
    -i /path/to/genomes \
    -g /path/to/schema \
    -o /path/to/output \
    --cpu 8

# Or with pre-computed CDS (pyrodigal, for exact comparison with chewBBACA)
python predict_cds.py \
    -i /path/to/genomes \
    -g /path/to/schema \
    -o /path/to/cds_output

chewcall \
    -i /path/to/genomes \
    -g /path/to/schema \
    -o /path/to/output \
    --cpu 8 \
    --cds-input /path/to/cds_output

Full options

chewcall [OPTIONS] -i <INPUT> -g <SCHEMA> -o <OUTPUT>

Options:
  -i, --input <INPUT>           Input directory with genome FASTA files
  -g, --schema <SCHEMA>         Schema directory (chewBBACA format)
  -o, --output <OUTPUT>         Output directory
      --cpu <CPU>               Number of CPU threads [default: 1]
      --cds-input <CDS_INPUT>   Pre-computed CDS directory (skip built-in prediction)
      --mode <MODE>             Alignment mode: "fast" (parasail) or "compatible" (BLAST) [default: fast]
      --blastp-path <PATH>      Path to blastp binary (required for --mode compatible)
      --gpu                     Use GPU (CUDA) for Smith-Waterman alignment
      --update-schema           Append novel alleles (INF) to schema FASTA files in place
      --bsr <BSR>               BLAST Score Ratio threshold [default: 0.6]
      --size-threshold <SIZE>   Size threshold for ASM/ALM [default: 0.2]
      --min-length <MIN>        Minimum sequence length [default: 0]
  -t, --translation-table <TT>  Genetic code [default: 11]
      --prodigal-mode <MODE>    Prodigal mode: single or meta [default: single]

CDS prediction modes

chewcall supports three CDS prediction modes:

1. Built-in prodigal-rs (default) — Pure Rust reimplementation of Prodigal 2.6.3 (single mode). No external dependencies. Uses the .trn training file from the schema directory.
2. Pre-computed CDS (--cds-input) — Reads CDS from a directory of FASTA files pre-computed with pyrodigal or prodigal.
3. External prodigal (--prodigal-path) — Spawns prodigal as a subprocess for each genome.

Schema compatibility

chewcall works with any schema in the standard chewBBACA format:

schema/
├── locus1.fasta          # Full allele sequences
├── locus2.fasta
├── short/
│   ├── locus1_short.fasta  # Representative alleles
│   └── locus2_short.fasta
└── *.trn                 # Prodigal training file

Schemas can be downloaded from Chewie-NS or prepared with chewBBACA's PrepExternalSchema / CreateSchema.

chewBBACA.py DownloadSchema -sp <species_id> -sc <schema_id> -o schema_dir

Output files

File	Description
results_alleles.tsv	Allelic profiles (locus x genome matrix)
results_alleles_hashed.tsv	CRC32-hashed allelic profiles
results_statistics.tsv	Per-genome classification statistics
loci_summary_stats.tsv	Per-locus classification counts
results_contigsInfo.tsv	CDS coordinates on contigs
novel_alleles.fasta	Novel allele sequences (INF)

License

GPL-3.0 — same as the original chewBBACA.

Authors

GenPat Team — Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise