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
FRC output
Coverage distribution
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
EDIT
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 :