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?
•
written
by
Dee •
1 answer
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.
Log in to answer this question.
-
Linking AMR Genes to Taxonomy in Soil Metagenomics
written by LuciaNhu •
-
Metagenomic Binning: before or after denovo assembly?
written by gatheringdusthere •
-
How do we know that our contig sequence is really plasmid?
written by rickyalfaray •
-
How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
written by O.rka
-
Identify sample mix from NGS data
written by Boberoni •
-
Can I assemble a bunch of contigs of a bacterial genome to get the full genome sequence?
written by AnonymousEngineer •
-
Unequally pooling libraries for RNAseq?
written by jingjin2203 •
-
Remove contamination before assembly
written by bruseq •
-
Problem with WGS
written by aggsandy8 •
-
Where does my RNASeq contamination fits on the Tree of Life?
written by Biomonika (Noolean)
