Remapping assembled contigs from Flye output file

Question

[synthiiihuh]

I have a bacterial assembled fasta file done using flye. I wanted to know how I can remap this assembled contigs against a reference genome as the number of contigs are very high.

[GenoMax]

how I can remap this assembled contigs against a reference genome as the number of contigs are very high.

That may indicate a "not so well" assembled genome. Perhaps that is what you are trying to determine by the mapping.

Answer 1

[lieven.sterck]

Plenty of tools to choose from: MUMmer, Mauve, Lastz, .... just to name a few.

Google with the term 'genome to genome alignment' will give you several other options.

Answer 2

[colindaven]

You can map contigs vs a related reference genome with a tool like Ragtag https://github.com/malonge/RagTag. This scaffolding makes more sense than just general contig mapping.