v0.4.0

Duplex calling

Bonito duplex calling for crf-ctc models. This method takes template & complement pairs to produce higher quality calls.

$ bonito duplex dna_r9.4.1 /data/reads --pairs pairs.txt --reference ref.mmi > basecalls.sam

The pairs.csv file is expected to contain pairs of read-ids per line (separated by a single space).

Follow-on reads can also be automatically paired if an alignment summary file is provided instead of a pairs.csv.

$ bonito duplex dna_r9.4.1 /data/reads --summary alignment_summary.txt --reference ref.mmi > basecalls

The duplex caller replaces the older bonito pair interface and builds on the work from @jordisr and @ihh ¹.

1. Silvestre-Ryan, J., Holmes, I. Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing. Genome Biol 22, 38 (2021). https://doi.org/10.1186/s13059-020-02255-1