Question: Annotation of assembled metagenomic data
2
gravatar for lagartija
16 months ago by
lagartija80
lagartija80 wrote:

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,

taxonomy metagenomics • 684 views
ADD COMMENTlink modified 16 months ago by Juke344.1k • written 16 months ago by lagartija80
1

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

ADD REPLYlink written 16 months ago by Joe16k
2
gravatar for Juke34
16 months ago by
Juke344.1k
Sweden
Juke344.1k wrote:

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.

ADD COMMENTlink modified 16 months ago • written 16 months ago by Juke344.1k

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.

ADD REPLYlink written 16 months ago by lagartija80
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