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Annotation of assembled metagenomic data

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,

metagenomics taxonomy
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updated by Juke34 Juke34 • written by lagartija lagartija

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

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written by Joe Joe

1 answer

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.

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written by Juke34 Juke34

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.

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written by lagartija lagartija

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