Almost correct. The thing is, the assembly may be incomplete, meaning that the genome might be larger than 2 Mb. You should divide by the estimated genome size, if you know it. There are also ways to estimate it using a k-mer analysis (e.g. GenomeScope). However, it looks like your data is extremely deep, so the assembly size you got is probably close to the real genome size, so looks like you have an average sequencing depth of ~3000x.
How is genome coverage / depth is determined?
I have the raw R1 and R2 files of a bacterial genome sequence that have been assembled into contigs using spades. How can I calculate the genome coverage / depth? Thanks.
• 2,079 views
•
link
written
by
dnaproteinstudy •
1 answer
There seems to be ~ 40000000 raw reads (including both R1 and R2) of 150 bp paired end sequencing and after spades assembly the size is ~2000000 nucleotides. So its 3000x coverage?
• 0 views
•
link
written
by
dnaproteinstudy •
Thank you so much. I am a newbie to this research, but I'll try if I can find it using GenomeScope in Galaxy.
• 0 views
•
link
written
by
dnaproteinstudy •
@liorglic, sequencing depth of ~3000x is normal?
• 0 views
•
link
written
by
dnaproteinstudy •
Thank you
• 0 views
•
link
written
by
dnaproteinstudy •
Log in to answer this question.
More posts like this
-
How to get a consensus of the contigs obtained from an assembler like spades?
written by DanielC
-
Criteria for filtering contigs after spades assembly
written by fhsantanna
-
Alignment of mutli-contig fasta files
written by L Ron Hubbard •
-
Extracting unmapped reads to draft genome
written by Bioinfonext
-
Split fasta file into chromosomes
written by natasha
-
High coverage bacterial genome reads causing spurious assemblies
written by b2060780 •
-
metavirome coverage with spades assembler
written by scarabbeetle •
-
How do I access genome coverage using SPADES?
written by fhsantanna
-
No Bowtie Alignments
written by hollynns •
-
Close Bacterial Draft Genome With Other Draft Genome
written by biotech
