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kishwarshafin / helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
MIT License
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Compatibility with draft assembly from other assemblers #19

Closed SHuang-Broad closed 4 years ago

SHuang-Broad commented 4 years ago

Hi,

I'm wondering if M + H is compatible with draft assemblies from other assemblers. It would be great if there's already some documents showing comparisons.

Thanks! Steve

kishwarshafin commented 4 years ago

Hi @SHuang-Broad ,

Yes, MP-HELEN is compatible with other assemblers as we have shown in our paper, Figure 4c.

We expect to see the same level of improvement with any assembler you use. Also, we are going to do v1.0 release in 2-3 days. If you are planning on using it, I would recommend waiting until the end of this week.

For your reference, here's the comparison:

Screen Shot 2020-03-02 at 6 02 13 PM
SHuang-Broad commented 4 years ago

Nice!

I do have multiple haploid assemblies and would like to see how to improve QV with polishers. I'll keep an eye on the new release.

Thank you for the detailed explanation!

kishwarshafin commented 4 years ago

@SHuang-Broad ,

I have pushed the latest version to master. Please use the local installation method for now. We are doing some internal comparison with other pipelines, once that is done, we'll do the official release with results.

I would also point you out to PEPPER (https://github.com/kishwarshafin/pepper). We are getting very competitive results with PEPPER and MP-HELEN. Please let me know if you have any issues. If you have the bandwidth, please try both tools and let us know how the assembly looks post polishing.