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rkajitani / MetaPlatanus

De novo metagenome assembler
GNU General Public License v3.0
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Some clarification about MetaPlatanus pipeline #12

Closed kafker closed 2 years ago

kafker commented 2 years ago

Dear Devs,

Thank you for MetaPlatanus, it is a nice addition to the few pipeline out there that use both Illumina and long-reads for metagenome assembly. I have a question regarding the use of NextPolish after the binning step with MetaBAT2.

Given the high error rate of long-reads, especially ONT reads, this could, in theory, affect the TNF of some scaffolds and therefore, MetaBAT binning. For this reason, wouldn't be more advisable running the polishing step after the scaffolding step?

Thank you!

rkajitani commented 2 years ago

Sorry for the late reply. MetaPlatanus firstly assembles contigs from Illumna reads, and it uses long reads only for scaffolding before MetaBAT binning. After binning, it closes gaps by long reads. Therefore, regions assembled from long reads, which may consist of many errors, are not used for binning.

kafker commented 2 years ago

Sorry for the late reply. MetaPlatanus firstly assembles contigs from Illumna reads, and it uses long reads only for scaffolding before MetaBAT binning. After binning, it closes gaps by long reads. Therefore, regions assembled from long reads, which may consist of many errors, are not used for binning.

Thanks for the clarification Rei.