No contig output for local assembly

[GuillaumeHolley]

Hello,

I am trying to assemble the ONT reads overlapping a specific region of the human genome and unfortunately, in this region, I end up with only 4 reads (3 of which have a length below 5 kbp). After running wtdbg2 and wtpoa-cns, I get no contig.

The end of wtdbg2 log indicates:

searched 1 contigs
Estimated:
output 0 contigs

and wtpoa-cns log indicates:

0 contigs 1 edges

I am using the following parameters for the assembly:

-p 0 -k 15 -AS 1 --edge-min 1 --rescue-low-cov-edges

Do you know what is happening here (too low coverage?) and if I can do something to solve the issue (some parameters I didn't think about)? I also tried to decrease -k and -l without success.

Thank you for your help.

Guillaume

[ruanjue]

Please have a look at --ctg-min-length, --ctg-min-nodes in wtdbg2 --help. Since your input was 4 reads, please generate a assembly-graph image from prefix.3.dot using dot -Tpdf -O .... If you have question about the dot graph, please contact me.

[GuillaumeHolley]

Thank you for your input. Both parameters helped a lot for a few use-cases I had.