Script to convert output to AGP format?

[Kate Taylor]

Redundans has done great things for my assembly, so thank you for making it! 

My apologies for asking a very basic question. 

I would like an AGP v2 file format describing my assembly from Redundans. I am new to this file format so may be missing an obvious way to generate it. The Redundans output file "scaffolds.longreads.1.fa.tsv" seems to contain some of the necessary information to generate an AGP file as it describes which contigs make up each scaffold. However, it looks like a significant coding challenge to do the conversion to me. I am wondering if someone in the community has a script that converts a redundans output file to AGP format that they would be willing to share or if there is some other way redundans users are making AGP files. 

Thank you for any guidance!

Kate

[Leszek]

Dear Kate, frankly I've never done AGP for redundans output. What you can try is to split your scaffolds at gaps and generate AGP from there (see fasta2agp.py). NOTE, this AGP will not correspond to your initial contigs, but it'll just inform where are the gaps in you final scaffolds, so it's not exactly what you need... Still, it may help :)

btw, sorry for late reply - just started new position last month.

Greetings from Barcelona!

L.

---

To stay up-to-date with #NGSchool follow us on Facebook and on Twitter.

--
You received this message because you are subscribed to the Google Groups "Redundans" group.
To unsubscribe from this group and stop receiving emails from it, send an email to redundans+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/redundans/68b1fbf4-b1a3-4079-8e92-2017b973da65%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.