Closed iek closed 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
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/
?