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Nanopolish without reference genome jordi Bioinformatics 0 01-26-2017 07:51 AM

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Old 09-19-2017, 06:16 AM   #1
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Location: Paris

Join Date: Sep 2017
Posts: 5
Default Nanopolish 1D

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

Last edited by anotherSAM; 09-20-2017 at 03:42 AM. Reason: typo
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Old 09-25-2017, 02:28 PM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 796

The 'ont2d' flag sets up BWA parameters to work for ONT data. It was named at a time when 2D data was similar accuracy to what 1D data is at the moment. You should be fine using Albacore 2.0-called reads with the stated workflow.

The indexing process links the Fast5 files to the FASTQ records. Nanopolish uses this index and the FAST5 files to correct the reads during the polishing step.
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canu, nanopolish, ont

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