How to run nucmer without reference? (viruses metagenomics)

Question

[Arsenal]

Hi!

I'm testing detection and abundance of viruses in metagenomics (viromics). In (Roux et al, 2017), The authors state the use of nucmer (from mummer) to cluster the contigs:

' Contigs from all samples were clustered with nucmer (Delcher, Salzberg & Phillippy, 2003) at ≥95% ANI across ≥80% of their lengths, as in (Brum et al., 2015; Gregory et al., 2016), to generate a pool of non-redundant “population contigs” '

Where I'm stuck:

• I have all my contigs from all the samples (which are grouped by experimental conditions) in only one denovo assembly file (with megahit). There is no reference; the samples come from mouse gut. Theoretically, there are several (probably unknown) genomes.
• nucmer has at least two obligatory multifasta inputs; a reference and the query.

What am I supposed to do?

• Merge a selection of viral genomes and use it as reference?
• Assemble the samples/groups separately and then use one assembly as reference?
• Use the same assembly file as both reference and query?
• Split the assembly file then use one (maybe the largest) contig as the reference?
• Anything else?

Alternatively, I've performed clustering with CD-HIT. Would nucmer be better at clustering? I can only answer that if I could somehow run nucmer.

If anyone has good experience with another viromics pipeline, I would be happy to test it. Any help will be very much appreciated. Thanks!

[Arsenal]

Based on this post I guess the deal is aligning my contigs assembly file to itself.

Answer 1

[colindaven]

You might find something like MUGSY http://mugsy.sourceforge.net/ to be more efficient / an easier alternative than nucmer. While nucmer has produces very good alignments, I find it not that easy to automate in all vs all scenarios.

[Arsenal]

Thank you! But I have just seen that mugsy does use nucmer as well... The mugsy help simply has the same options of nucmer under the "-nucmeropts" parameter.

I still need to know what are the parameters to set the 'Contigs from all samples were clustered with nucmer (Delcher, Salzberg & Phillippy, 2003) at ≥95% ANI across ≥80% of their lengths, as in (Brum et al., 2015; Gregory et al., 2016), to generate a pool of non-redundant “population contigs” '

:(