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Deacon

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Search and depletion of FASTA/FASTQ files and streams using accelerated minimizer matching.

https://github.com/bede/deacon

DOI: https://doi.org/10.1101/2025.06.09.658732

MIT License

Deacon filters DNA sequences in FASTA/Q files and streams using SIMD-accelerated minimizer comparison against an indexed query. It can either keep matching sequences (search mode, default) or remove them (depletion mode, -d / --deplete). Built with panhuman host depletion in mind but useful for searching large sequence collections.

This module parses the JSON summary log written by deacon filter when called with -s / --summary, and reports the number of input, kept, and removed sequences and base pairs alongside the filter mode.

Generating compatible output​

The module looks for the JSON summary file produced by the --summary (-s) option:

# Search mode: keep matching reads
deacon filter index.idx reads.fq.gz -o matches.fq.gz -s summary.json

# Depletion mode: remove matching reads (e.g. host depletion)
deacon filter -d panhuman-1.k31w15.idx reads.fq.gz -o depleted.fq.gz -s summary.json

Interpreting results​

seqs_removed and bp_removed count sequences and base pairs that matched the indexed query and were therefore filtered out. In depletion mode (Deplete = True) these are typically host reads to discard; in search mode they are non-target reads. The Deplete column distinguishes the two modes so the same report can mix search and depletion samples.

File search patterns​

deacon:
  contents: '"version": "deacon'
  fn: '*.json'
  num_lines: 30
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