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Remapping assembled contigs from Flye output file

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.

assembly remapping flye
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updated by Ram Ram • written by synthiiihuh • synthiiihuh

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.

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written by GenoMax GenoMax

2 answers

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.

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written by lieven.sterck lieven.sterck

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.

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written by colindaven colindaven

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