Metagenomics with multiple references

[davidvilanova]

Hi,
Can i use the tool with a fasta reference file with different bacterial genomes ?
I’m trying to improve the model when running a metagenomics experiement, focusing only on most abundant (10 different bacterial genomes)

Thanks

[tmassingham-ont]

Hello. The reference file used to prepare a training set needs to contain a reference sequence specific to each read (trimmed and in the read's orientation). Provided you can confident map your reads to your fasta reference file, you can create the read-specific reference file using the get_refs_from_sam.py tool provided.

See https://github.com/nanoporetech/taiyaki#preparing-a-training-set

Hope this is useful.

TimM.