multiple rounds of Pilon polishing: need new bam file?

[ssully]

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?

[Gopo]

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.

https://gist.github.com/jelber2/0c7fc56fa71a7f45d1cef40b5946a393