Genome assembly contig ordering
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.
1 answer
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
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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.