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Old 02-26-2013, 08:35 AM   #6
severin
Genome Informatics Facility
 
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105
Default Nice tool

Sebastien,

This really is a nice tool. Sorry to bombard you with so many questions but I would like to know the limitations of the tools I am using. Some of the runs I have experienced where not all the contigs are assigned to a species. In which case wouldn't this lead to a misrepresentation of what is present in the sample?

How hard would it be to also output the relationship between contig and Taxonomic level? ... Order family genus etc

ie contig-001 Micrococcineae

In other cases every contig is assigned, in which case, how do we determine quality of match to a bacteria or virus if those are the genomes we are using when in actuality the contig belongs to a Eukaryote? Ie possible miss-assignment due to limited number of genomes in the search.

Finally, How does kmer length affect ability to assign a contig to a species/taxonomic group? Have you look at this?

Thanks for all your help on this.

Regards,

Andrew
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