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nanoporetech / taiyaki

Training models for basecalling Oxford Nanopore reads
https://nanoporetech.com/
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Metagenomics with multiple references #70

Open davidvilanova opened 4 years ago

davidvilanova commented 4 years ago

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 commented 4 years ago

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.