Right now we do not use the scaffolding step since we treat all reads as single reads.
Using paired-end reads could allow us to use the scaffolding step from SGA (not implemented yet in sga_assembly.py) and improve MATAM contigs length.
However, this mean that SGA would generate scaffolds with Ns and we have to evaluate how to handle those.
ppericard
commented
7 years ago
Right now we do not use the scaffolding step since we treat all reads as single reads. Using paired-end reads could allow us to use the scaffolding step from SGA (not implemented yet in sga_assembly.py) and improve MATAM contigs length. However, this mean that SGA would generate scaffolds with Ns and we have to evaluate how to handle those.