Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Decreasing minimum required read coverage for assembly #84

Open
chocotwig opened this issue Apr 14, 2020 · 0 comments
Open

Decreasing minimum required read coverage for assembly #84

chocotwig opened this issue Apr 14, 2020 · 0 comments

Comments

@chocotwig
Copy link

Hi,

I observe that while I can manually draw out a single path between, say 5 reads, miniasm only generates a contig that has >2x read coverage at all locations along its length (not including the hanging ends of the terminal reads either). Eg. my 5 reads correspond to a genomic region with the left to right sequence of this region consisting of three segments as such: LEFT-MIDDLE-RIGHT. LEFT and RIGHT have 2x read coverage and MIDDLE, which connects both segments with large overlap, has only 1x read coverage. So miniasm only reports contigs corresponding to LEFT and RIGHT, ignoring the 1x covered MIDDLE.
How can I make miniasm also include the 1x covered MIDDLE, and report a contig of the form LEFT-MIDDLE-RIGHT?

Thanks!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant