Taxonomic binning of assembly from WGS

Question

[Dee]

Hi,

I’m trying to identify a cyanobacteria from the genome assembly of whole genome sequences (i.e. single organism). However, GTDB cannot identify it and shows very high contamination when I used my assembled sequences as input. The samples were extracted from unialgal cultures (and other bacteria may be present). I’m wondering if anyone has tried to perform taxonomic binning from the genome assembly of WGS to determine the taxonomic classification of the bacteria from the samples, and would you recommend doing this method?

Answer 1

[Mensur Dlakic]

GTDB doesn't work with highly contaminated samples. One can do binning by tetra-nucleotide frequencies, which in most cases will separate the samples taxonomically. After that GTDB should be able to classify the bins.

https://bitbucket.org/berkeleylab/metabat/src/master/