Orienting contigs/ scaffolds in de novo assembly
0
0
Entering edit mode
2.8 years ago
Yuyayuya ▴ 180

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 • 1.6k views
ADD COMMENT
2
Entering edit mode

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 REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1833 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6