v0.5.0

Highlights

• Modified basecalling via Remora.
• Aligned/unaligned SAM/BAM/CRAM output support with read groups (draft spec).
• Fast/HAC/SUP models for R9.4.1 E8, R9.4.1 E8.1 and R10.4 E8.1.
• Model performance for SUP & HAC models are now inline with Guppy.
• Fully calibrated qstring/qscores for all models.
• Automatic model downloading.

Modified Basecalling

Methylation/modified base calling can now be enabled with a single flag --modified-bases.

$ bonito basecaller [email protected] reads --modified-bases 5mC --ref ref.mmi | samtools sort -o out.bam -
$ samtools index out.bam
$ modbam2bed -a 0.2 -b 0.8 --cpg -r chr20 -m 5mC -e ref.fa out.bam > results_5mC.bed

Models

All model identifiers include the model version, ambiguous unversioned models are no longer provided.

Condition	Fast	High Accuracy	Super Accuracy
R9.4.1 E8	[email protected]	[email protected]	[email protected]
R9.4.1 E8.1	[email protected]	[email protected]	[email protected]
R10.4 E8.1	[email protected]	[email protected]	[email protected]

Available models can be listed with bonito download --models --list.

v3.4 models are newly released whereas v3.3 models have been available previously, however, all models have newly tuned configs. Fast models are now higher accuracy 128 wide models.

Models configs have been tuned for performance and the batch sizes have been selected to use approximately 11GB of GPU memory. If you have a GPU with less than this please reduce the batch size with --batchsize when base calling.

Misc

• CUDA 11.3 builds added.
• Updated dependency highlights: pytorch==1.10, mappy=2.23.
• Duplex calling superseded by significantly higher performance inplmention in Guppy 6.0.
• Basecaller default parameters can now be set in the model config.toml under the [basecaller] section
• Command line parameters will now override config.toml settings.
• SAM tags included when output .fastq (SAM/BAM/CRAM is recommended however).

Full Changelog: v0.4.0...v0.5.0