Question: Orienting contigs/ scaffolds in de novo assembly
0
gravatar for Yuyayuya
4 months ago by
Yuyayuya80
USA
Yuyayuya80 wrote:

Hello everyone, I'm doing de novo assembly from 150 bp whole genome shotgun reads. My pipeline is:

  1. Trimmomatic (trimming and quality filtering)
  2. SOAPdenovo2 (de novo assembly)
  3. mumMER3 (align to reference sequence).

After aligning contigs to reference sequence, I connect the contigs according to their order. My problem is how to make all contigs in the same orientation?

Thank you!

assembly • 254 views
ADD COMMENTlink written 4 months ago by Yuyayuya80
2

There is a range of contig reordering tools available:

However, if you're already using Mummer, then you could look into the show-tiling option as it can also fix order and orientation and can generate a pseudo-sequence when -p filename Output a pseudo molecule of the query contigs to file option is specified.

ADD REPLYlink modified 4 months ago • written 4 months ago by Sej Modha3.8k
1

I think one possible way could be the reverse complement of your contig.

ADD REPLYlink written 4 months ago by Nitin Narwade310
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