Question: Genome assembly contig ordering
0
gravatar for mittu1602
23 months ago by
mittu1602150
India
mittu1602150 wrote:

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.

assembly genome • 1.1k views
ADD COMMENTlink modified 11 days ago by Biostar ♦♦ 20 • written 23 months ago by mittu1602150

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.

ADD REPLYlink written 11 days ago by harish200
4
gravatar for Paul
23 months ago by
Paul80
India
Paul80 wrote:

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.

ADD COMMENTlink modified 23 months ago • written 23 months ago by Paul80

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

ADD REPLYlink written 23 months ago by barrypraveen20
1

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

ADD REPLYlink modified 23 months ago • written 23 months ago by Paul80

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

ADD REPLYlink written 23 months ago by Paul80

I'll look into this, Thank you.

ADD REPLYlink written 23 months ago by mittu1602150

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

ADD REPLYlink written 23 months ago by mittu1602150
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