I had a question for the community.
I have a genome of a new species that has been sequenced via 150pb Illumina paired-end.
To verify the quality of the assembly I used the
BUSCO pipeline which allows me to search for 99% of the BUSCO genes (gene not duplicated) present in a taxon in the genome of my species.
Globally I only miss
18% of the BUSCO genes, which means that the assembly is not too bad.
Now when I plot the G+C% and the coverage of all the scaffolds containing BUSCO genes (so a priori non-contaminating) I should find a fairly homogeneous cloud.
Instead I end up with two different coverage profiles (noted red and blue below):
I then thought that the low coverage sequencing profile around 4x might be a eukaryotic contaminant like a acarians, however when I blast the BUSCOs present on these low coverage scaffolds I get hits that are very close to the genome of my species...
Does anyone have any idea what these are?
here is an output of the
contigsTable.csv where the two first row are scaffold with low coverage in the figure, and two last are scaffold with high coverage in the figure
Here is an Icarus summary of the assembly :
Assembly # contigs (>= 0 bp) 1038631 # contigs (>= 1000 bp) 120132 # contigs (>= 5000 bp) 22245 # contigs (>= 10000 bp) 9986 # contigs (>= 25000 bp) 1322 # contigs (>= 50000 bp) 97 Total length (>= 0 bp) 655530043 Total length (>= 1000 bp) 451497861 Total length (>= 5000 bp) 260894112 Total length (>= 10000 bp) 174183054 Total length (>= 25000 bp) 45006012 Total length (>= 50000 bp) 5956145 # contigs 214542 Largest contig 120620 Total length 519138286 GC (%) 32.94 N50 5062 N75 1624 L50 21982 L75 71030 # N's per 100 kbp 22.28
Here is the BUSCO summary as well :
2544 Complete BUSCOs (C) 2312 Complete and single-copy BUSCOs (S) 232 Complete and duplicated BUSCOs (D) 1060 Fragmented BUSCOs (F) 811 Missing BUSCOs (M) 4415 Total BUSCO groups searched C:57.7%[S:52.4%,D:5.3%],F:24.0%,M:18.3%,n:4415
I ran the fastq sequences with another aligner (MEGAHIT) to see if it was not because of an assembly issue and I got the same profils coverage see here :