Genome assembly contig ordering

Question

[mittu1602]

Hello,

I am working with single-end genome assembly of a fungal species generated by ion-torrent PGM, I have assembled draft stage by de-novo technique using SPAdes assembly tool. I am looking for contig ordering tools without reference since its a de-novo assembly process.

Thank you.

[harish]

You can scaffold them using many tools like BESST, SSPACE etc.

However, ideally it wouldn't matter how you order the contigs (method), as there are many methods available. Does your organism have a closely related species preferably in chromosome? If yes, then you can RaGOO.

Answer 1

[Paul]

Use SSPACE.

https://academic.oup.com/bioinformatics/article/27/4/578/197626/Scaffolding-pre-assembled-contigs-using-SSPACE

https://github.com/nsoranzo/sspace_basic

You need to put the contigs in scaffolds.

[PK]

During assembly If the gap is high what about the performance of SSPACE?

[Paul]

You can benchmark scaffolding your contigs using various tools, and choose the one with the best output

One such tool is: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

However, If the gaps are still high, it could be due to low-coverage sequencing data

[Paul]

If an answer is helpful, upvote it. If the answer resolved your question, mark it as accepted.

[mittu1602]

I'll look into this, Thank you.

[mittu1602]

yes, have already made contigs into scaffolds and also SSPACE is for paired end data. Thank you