bfscan 0.0.3

bfscan is designed to detect foodborne pathogens using bloom filter and machine learning

bfscan

BFScan is a tool to scan FASTA and FASTQ files using a combination of k-mer composition, Bloom-filter and machine learning methods.

Example

1. Construction a collection of Bloom filters for targets organisms

$ bfscan-build-filters \
    -i \
        data/fasta/salmonella.fasta \
        data/fasta/listeria.fasta \
        data/fasta/campylobacter.fasta \
    -o data/filters/filter

2. Training a machine learning model

$ bfscan-build-model \
    -i \
        data/fasta/salmonella.fasta \
        data/fasta/listeria.fasta \
        data/fasta/campylobacter.fasta \
    -o data/models/model \
    -background data/fastq/metagenome.fastq \
    -r data/reports/classification_report.txt

3. Running the search

$ bfscan-search \
    -i \
        reads.fastq \
    -o data/results/filtered \
    -F fastq
``