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VGP / vgp-assembly

VGP repository for the genome assembly working group
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Pipeline for Polishing Canu assembly with Illumina Reads #80

Closed iek closed 1 year ago

iek commented 2 years ago

Hello, I'm sorry for the inconvenience, but is there a tutorial somewhere on how to polish a Canu assembly of Nanopore reads using Illumina reads? The Canu github linked me to here: https://github.com/VGP/vgp-assembly/tree/master/pipeline/freebayes-polish . However, I don't see a tutorial on how to exactly begin polishing.

Do I perhaps just use the following command: ./_submit_longranger_freebayes.sh assembly.fasta reference_genome.fasta along with putting the illumina reads in /data/rhiea/<genome>/genomic_data/?

arangrhie commented 1 year ago

Hello, apologies for the very delayed response! There are multiple ways to polish - the freebayes pipeline being one of it, which however, the pipeline linked would assume using linked-reads (longranger part).

Try align your Illumina reads with the bwa mem pipeline instead, then call variants (SNV errors) with either freebayes, GATK or DeepVariant.

My current best-practice for a regular Canu ONT assembly (not phased) would be using DeepVariant + Merfin.

Best, Arang