Nanopore reads

[mccartneya90]

Heya,

I was just wondering if this could be utilised on nanopore assemblies? and if so what parameter I should specify for READ_TYPE in the snakemake.yml file.

Many thanks,
Ann

[a-ludi]

Hi Ann,

yes, it can be used with nanopore reads (and assemblies). Basically, you can specify anything other than PACBIO_SMRT but I would recommend using OXFORD_NANOPORE as NCBI does.

Rationale

PacBio use a specific header format for their reads which is parsed by fasta2DB. Consequently, it cannot be applied to Nanopore-style FASTA files. As of now, the read_type parameter just determines whether to use fasta2DB or fasta2DAM when converting the reads to a Dazzler DB.

[a-ludi]

A section about using nanopore reads should be added to the README.

[mccartneya90]

Brilliant! Thank you so much for all of the help and advice. I really appreciate how promptly you've gotten back to me on this. A