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ziyewang / COMEBin

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Compare with metabinner #19

Open PonderLi opened 5 months ago

PonderLi commented 5 months ago

Hello, thank you very much for providing such an excellent binning tool. I have noticed that Metabinner also originates from your team. Could you please share your recommendation on which one you would suggest using? Thank you very much!

ziyewang commented 5 months ago

Hi,

Both MetaBinner and COMEBin are more suitable for prokaryotic genomes, but COMEBin can recover not only prokaryotic genomes. Based on our experience, COMEBin performs better on single-sample or few-sample second-generation data, while MetaBinner performs well on third-generation data. As for multi-sample second-generation data, both perform reasonably well. However, considering runtime, COMEBin is recommended for use in a GPU environment.

Best, Ziye

PonderLi commented 5 months ago

Hi,

Both MetaBinner and COMEBin are more suitable for prokaryotic genomes, but COMEBin can recover not only prokaryotic genomes. Based on our experience, COMEBin performs better on single-sample or few-sample second-generation data, while MetaBinner performs well on third-generation data. As for multi-sample second-generation data, both perform reasonably well. However, considering runtime, COMEBin is recommended for use in a GPU environment.

Best, Ziye

THANKS for so quick reply！ It is so helpful for me to choose better binning tools by your suggestion. But now I have another question, is it necessary to dereplicate the contigs (eg, from MEGAHIT) before binning by COMEBin? Some binning tools need all contigs to get coverage. Does COMEbin have same requirement?

ziyewang commented 4 months ago

COMEBin does not need all the contigs to get coverage, but in most cases, we only remove short contigs.

PonderLi commented 4 months ago

COMEBin does not need all the contigs to get coverage, but in most cases, we only remove short contigs.

Thank you for your enthusiastic response, and I apologize for having one last question. How do I perform multi-sample binning using COMEBin? I couldn't find it in the benchmark. Thank you for your patient reply, and I wish you success in everything.

ziyewang commented 4 months ago

Hi, In multi-sample binning, users are required to provide the contigs from each individual sample along with the corresponding BAM files that encompass all related samples. The number of BAM files should match the number of related samples.

The commands to run the binning methods are the same as the single sample mode, except for replacing the single-sample bamfile with the bamfiles of all corresponding samples.

Please refer to the following commands for performing multi-sample binning using COMEBin.(https://github.com/ziyewang/COMEBin_benchmark/tree/master/benchmark).

Best, Ziye