Evaluate assembly quality using Falcon

Question

[Rox]

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

[GenoMax]

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

[GenoMax]

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

$ grep -c "^>" your_file

[Rox]

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