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Old 04-22-2018, 05:12 AM   #1
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Default tools for merging assembled genome

Hi, All,

I have two assembled genome files:

1. Illumina reads were subject to MIRA and the resultant assembly file is very fragmented.
2. PacBio reads were subjected to Canu and Quiver, and then further polished with Pilon.

I wonder if there is a way to merge those genome files to increase the continuity (reduce the number of scaffolds).

Thank you very much for any inputs.

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Old 04-22-2018, 05:31 AM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 835

If you don't care about accuracy, just concatenate all the fasta sequences into a single large sequence....

More seriously, you're probably not going to get any better continuity from your data beyond what you've got with the PacBio reads.

How did you do the polishing with Pilon? I usually use that for correcting assemblies with Illumina reads, and that's how I would merge Illumina and PacBio reads for a genome assembly.

Last edited by gringer; 04-22-2018 at 05:34 AM.
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Old 04-22-2018, 09:54 AM   #3
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Surely, I do care about accuracy!

Pilon used bam files, which contains the information about the mapped reads. But the independent Illumina contigs contain much more information than that. That's why I am looking for the merge tools.
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