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Evaluate assembly quality using Falcon

Hi everyone !

I'm new to genome assembly. I used the diploid assembler Falcon on my PacBio data, because there is a lot of polymorphism in the studied species, and I want to visualize the fasta files Falcon created.

I was used to see assembly results using the Quast tool, but it's not working well in my case.

As the file is big (270Mo) and contain just one line, I can't really just open it in Gedit or something. So I can't really figure out how the contigs are separated, and how the file looks like in the inside.

Does anyone have a advice about it ?

Thanks for your answers !

Cheers,

Roxane

assembly
• 1,925 views • link
written by Rox Rox

Use one of the methods to convert your giant file into individual fasta files (I assume the file does not contain one line otherwise you would have a single giant contig). If there are hundreds of contigs then be ready for a boatload of files:

How To Split A Multiple Fasta
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
how to convert a long fasta-file into many separate single fasta sequences

• 1 views • link
written by GenoMax GenoMax

You could get a count of how many contigs there are by doing

$ grep -c "^>" your_file
• 1 views • link
written by GenoMax GenoMax

Thanks a lot ! That should help, I'm going to try this, thanks again genomax2 !

• 1 views • link
written by Rox Rox

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