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bcgsc / ntedit_sealer_protocol

Efficient targeted error resolution and automated finishing of long-read genome assemblies
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Multiple short read libraries #6

Closed aabaricalla closed 2 years ago

aabaricalla commented 2 years ago

Hello, I recently discovered this pipeline and I'm already testing it with my data. Reading the paper and the Help page, I assumed you can pass only one pair-end library. Can I use another additional library? e.g.: reads='lib1_1.fq.gz lib1_2.fq.gz lib2_1.fq.gz lib2_2.fq.gz' Or with the deeper library available, it's enough? Thanks!

lcoombe commented 2 years ago

Hi @aabaricalla,

Just checking - is this a different library from the same sample? If so, then yes you could certainly pass the additional reads to the polishing protocol. Whether it would make a big difference to the overall polishing would depend on the coverage of the reads that you're using.

Hope that helps - thank you for your interest in the ntEdit+Sealer protocol! Lauren

aabaricalla commented 2 years ago

Thanks @lcoombe! As you said, it's from the same sequencing project. I'll try both, with just one or with a couple of libs. I'll be sharing my results as soon as I get it. Cheers!