Orienting contigs/ scaffolds in de novo assembly
Hello everyone, I'm doing de novo assembly from 150 bp whole genome shotgun reads. My pipeline is:
- Trimmomatic (trimming and quality filtering)
- SOAPdenovo2 (de novo assembly)
- 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!
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Yuyayuya •
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I think one possible way could be the reverse complement of your contig.
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 fileoption is specified.