Test for Dorado basecaller

[akikuno]

Describe the features you want.

Current DAJIN2 assumes base calling with Guppy, but it is necessary to confirm whether it works similarly with Dorado.

Describe the solution you'd like if you have any.

Try basecall and demultiplex using Dorado

DAJIN2 version

0.4.6

Additional context

None

[akikuno]

In Dorado, unlike Guppy, the output is in BAM format.

Considering that Dorado is likely to become mainstream in the future, it is better to primarily support Dorado. The input should accept BAM files and convert them to FASTQ internally.

For Guppy, the FASTQ files are output inside the barcodeXX directory. In the case of Guppy, it might be good to allow directory input by adding a --guppyoption.

[akikuno]

The input for dorado correct is FASTQ, and the output is FASTA, so it should be compatible with FASTA, FASTQ, and BAM inputs.

• [x] FASTA
• [x] FASTQ
• [x] BAM

[akikuno]

Completed in DAJIN2 v0.5.1.