Scaffolding without Illumina reads

[ATVincent]

Hello,

First, I want to thank you for this remarkable tool.

I used Redundans with only PacBio reads since I do not have Illumina reads. Here is the command:

../redundans/redundans/redundans.py -v -t 6 --log LOG.redundans -l Reads_?.fastq -f contigs.fasta -o redundans_results

I was surprised to realize that Redundans can generate scaffolds without having pairing information provided by Illumina reads. Can I have some explications ? How it can determines the number of "N" ?

Thank you

[lpryszcz]

Hi, thanks for the nice words!
Redundans uses pyScaf for long-read & reference based scaffolding. Since you have only long reads, you can try DBG2OLC. It worked quite well for me on some data (better than pyScaf;) ).
Let me know how it worked!