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Scaffolding not working #38

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fergsc opened this issue Aug 8, 2022 · 0 comments

fergsc commented Aug 8, 2022

Hi,

I am trying to scaffold an ONT assembled plant genome with pore-c.

My un-scaffolded genome is 639.15 Mbp, N50: 1.87 Mbp, number contigs: 564.

Pore-C sequencing resulted in the generation of 156.67 Gbp of data in 137,662,189 reads, N50: 1.38 Kbp.

After running the pore-c snakemake pipeline - https://github.com/nanoporetech/Pore-C-Snakemake - and scaffolding with SALSA, my genome is now: 415 sequences with an N50 of 2.44 Mbp.

Has anyone been able to successfully scaffold and have any tips for achieving success?

Thanks.

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