deacon 0.16.0rc1

Fast DNA search and [host] depletion using minimizers

Deacon Python bindings

Enables index reuse between filtering sessions.

from deacon import Index

index = Index("panhuman-1.k31w15.idx")
stats = [
    index.filter(fq, deplete=True, rename=True,
                 output=fq.replace(".fastq.gz", ".clean.fastq.gz"))
    for fq in input_fastqs
]
print(stats[0]["seqs_in"], stats[0]["seqs_out"])

filter accepts single or paired input (fastq2=, output2=), auto-detects .gz/.zst/ .xz output compression from the extension, and returns a dict of summary statistics. from deacon import filter also exposes filter(index, ...) as a free function.