Assemble contigs into chromosomes

Question

[kschach2]

Hey everyone,

I'm utilizing 10x genomics long read data to try and assemble a pig genome for a new pig breed. I've performed the de novo assembly using supernova and aligned the contigs to the pig reference genome (Sscrofa11.1) using nucmer. I'd like to use these alignments to construct a reference fasta file consisting of assembled chromosomes, but I'm not sure how to go about this. Are there any good programs out there that can create this output file?

Thanks

Answer 1

[lieven.sterck]

The term you should use for searching is "reference based assembly/scaffolding". There are certainly tools around that do this sort of analysis . Can't promise though they will start from the nucmer alignments, most will likely use minimap2 (which is also a good tip to use in stead of nucmer, output can be configured to common dataformats easily).

If I remember correctly, I think eg. Flye can do this (does not take nucmer alignment as input though)