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bioinformatics-centre / kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
http://kaiju.binf.ku.dk
GNU General Public License v3.0
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Taxonomy assignment of predicted proteins #15

Closed davidvilanova closed 7 years ago

davidvilanova commented 7 years ago

Hi, I´m running an illumina metagenomics WGS experiment (2x150bp). I have assembled my metagenomes with Megahit and predicted genes using prodigal and converted those to proteins. Now I would like to assign the taxonomy of the proteins and was wondering if kaiju is suitable for that ? (using refSeq as a database).

( A second option would be to run hmm on a marker genes databases but i found this too restrictive at the moment since you may miss some species)., althought there are at least 4 to 5 databases of marker genes out there that could be used.

Thanks for your advice. david

pmenzel commented 7 years ago

Hi David, yes, you can use Kaiju for assigning your predicted protein sequences to the taxonomy. You can just use the fasta file with the predicted protein sequences as input and set option -p when you have amino acid sequences as input for Kaiju. best, Peter