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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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mapping tool #74

Closed jdmontenegro closed 5 years ago

jdmontenegro commented 6 years ago

Hi everyone, I am looking forward to using this tool to polish a raw PacBio assembly using my illumina reads. This is a non-model species with nearly 50% being repeats. The assembly has undergone 2 rounds of polishing using with the PacBio reads using Racon and now I would like to use pilon. However, when I map the illumina reads with bowtie2 I get 55% mapping efficiency, whereas mapping the same reads with minimap2 produces 80% mapping efficiency. I can see that for pilon BWA mem is the recommended tool, what parameters would you suggest for mapping?

Kind regards,

Juan Montenegro

w1bw commented 5 years ago

Bowtie2 isn't particularly good at maintaining pairing when dealing with lots of repeated content. In my experience, BWA does that better. Default "bwa mem" paramters should work well with paired illumina reads.