Annotation of assembled metagenomic data

Question

[lagartija]

Hi,

I have to assign contigs from assembled metagenoms to their taxa and I am looking for a tool that would go faster than a blast. From what I see most of the tools (like Kraken) seem to use the reads for the taxonomic annotation. I don't have access to the reads. Do you know an efficient tool that works on assembled data ?

Thanks,

[Joe]

I believe kraken is also capable of using contigs. Check the newer versions,

Answer 1

[Juke34]

Yes I think Kraken and Bracken can work with contig too. Otherwise as said here https://github.com/bioinformatics-centre/kaiju/issues/73 Kaiju can do the job.

[lagartija]

Thank you ! I didn't know Kaiju, it seems good. I think this is also possible with QIIME, MetaPhlAn or Clark but I don't know which one to choose. Maybe I should try some of them on a subset of my data to see which one is more suited.