Get statistics about an alignment done by Hifiasm

Question

[pablo]

Hi ,

I had consensus reads (ccs.bam) from a PacBio sequencing. I used the assembler hifiasm to create an assembly on these CCS. I got several .gfa files but I would like to get some statistics on the assembly : % mapped reads , size of the assembly ...

How could I do this?

Thanks

[WouterDeCoster]

I used the aligner hifiasm to create an assembly

hifiasm doesn't give you an alignment. You used an assembler to create an assembly.

[pablo]

You're right, I edited my post.

Do you have an idea about my question?

[GenoMax]

I would like to get some statistics on the assembly : % mapped reads , size of the assembly ...

You will need to take your original reads and map them back (minimap2) to the assembly you generated. Then generate stats. Size of the assembly should be easy to get as a part of samtools idxstats output of alignment data.