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Old 04-26-2019, 02:47 PM   #1
Location: NYC

Join Date: Aug 2010
Posts: 48
Default multiple rounds of Pilon polishing: need new bam file?

Pilon takes an assembly and one or more sorted .bam files of reads, as input.

When doing more than one round of Pilon polishing on an assembly, for the second round, do I first need to create a new .bam file using the .fasta output of the first round as template?

or can i just use the same .bam file as used the first round?
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Old 04-29-2019, 12:09 AM   #2
Location: Louisiana

Join Date: Nov 2013
Posts: 38

For the second round, you first need to create a new .bam file using the .fasta output of the first round as template.

Here is a script (hosted on GitHub gist) for running Pilon twice on a single computer with X number of threads.
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