Orienting contigs/ scaffolds in de novo assembly

Question

[Yuyayuya]

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!

[Sej Modha]

There is a range of contig reordering tools available:

• ABACAS
• Mauve

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.

[Nitin Narwade]

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