Question: Orienting contigs/ scaffolds in de novo assembly
gravatar for Yuyayuya
10 weeks ago by
Yuyayuya40 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 • 173 views
ADD COMMENTlink written 10 weeks ago by Yuyayuya40

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 10 weeks ago • written 10 weeks ago by Sej Modha3.6k

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

ADD REPLYlink written 10 weeks ago by nitinnarwade1504200
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1164 users visited in the last hour