Contigs Taxonomy from assembled metagenomes

Question

[David]

Hi, I have assembled a metagenome (actually a community Mock) and would like to get the taxonomy.

I have seen that some people get the reads mapped to the contigs and annotate them using kraken.

The thing is that i would like to use the contig length to get a better taxonommic resolution, rather than relying on reads mapped to the contigs.

What would you recommend ? Any free tool ?

I was thinking of blast the contigs against the refseq database.

Thanks for your comments.

[Sej Modha]

An alternative to BLAST would be to run DIAMOND instead which is much faster and can search against protein database.

[David]

Proteins would require that i do it on predicted orf from my contigs (after binning). I´m not sure what wold be the gain (other than speed and time) ??

[GenoMax]

DIAMOND can do blastx like searches. It is also much faster than regular blast.

[David]

Ok thanks for the update. Looks like a reasonable option.

How do you convert the blast/diamond output into a taxonomy assignment ?? I guess you will get many hits for one contig or protein and was wondering if there is any specific methodology to assign the taxonomy given by blast/diamond hits ??

[GenoMax]

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