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MadsAlbertsen / mmgenome

Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
https://kasperskytte.github.io/mmgenome2/
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Using contigs instead of scaffolds for the genome extraction workflow #27

Closed adityabandla closed 6 years ago

adityabandla commented 7 years ago

Hi,

I used MEGAHIT to assemble a sediment metagenome. However, I ran into issues with finding a suitable scaffolder for converting the contigs to scaffolds.

Can I go ahead with the mmgenome workflow only with contigs? Is there a recommended scaffolder for metagenomic contigs?

Thanks

Kirk3gaard commented 7 years ago

Hi Aditya Bandla

There is no need for scaffolding. The package works equally well for contigs.

adityabandla commented 7 years ago

Thanks Rasmus! I sequenced 27x samples across 2 lanes on the HiSeq (250bp). These samples are spatially related and I see differences in the relative proportions of my target organism (whose genomes I am trying to assemble).

I did a composite assembly i.e. combined reads across all 27x samples into a single file which was then assembled. I then mapped each sample individually back to the contigs to estimate coverage. Is this considered a valid approach?

Thanks for the advise!

Kirk3gaard commented 7 years ago

Hi Aditya Bandla

Yes that is often how we run it. Coassembly of all reads and then making coverage files for each of the samples by individual mapping.