Parameter tuning for small (~5k) plasmids

[fredyr]

Hi,

I'm looking to tune the parameters for wtdbg2 (or troubleshooting in general) for recovering a smaller plasmid (~5k in size, many reads with the entire plasmid contained) that miniasm finds, but I have so far not been able to get wtdbg2 to find it.

• Do you have any tips on which parameters would be most important to tune?
• What would be a good way to troubleshoot? Could I try and find if it is present in some of the intermediate files, like the [123] graphs?

Thanks in advance Fredrik

[ruanjue]

Have a look at wtdbg2 --help.

 --ctg-min-length <int>
   Min length of contigs to be output, 5000
 --ctg-min-nodes <int>
   Min num of nodes in a contig to be ouput, 3

[fredyr]

Thanks -- that did indeed seem to solve it! In my previous attempts I seem to have mixed up the -L parameter with --ctg-min-length.