I am working on 1D minion data, albacore 2.0 called, and attempting to use nanopolish on canu derived contigs.
I am trying to follow the github/readme files but find it hard.
First I am under the impression nanopolish uses raw fast5 files in order to polish but the initial step requires indexing of fastq files (albaore 2.0 step)
Secondly for the mapping stage 'bwa mem...', the only options are for ont2d data.
When are the fast5 files used if they are?
and how can I use nanopolish on 1D data?
Thanks in advance
I am trying to follow the github/readme files but find it hard.
First I am under the impression nanopolish uses raw fast5 files in order to polish but the initial step requires indexing of fastq files (albaore 2.0 step)
Secondly for the mapping stage 'bwa mem...', the only options are for ont2d data.
When are the fast5 files used if they are?
and how can I use nanopolish on 1D data?
Thanks in advance
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