Get statistics about an alignment done by Hifiasm
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Expect heterozygous variant from reads
written by pablo
-
Pacbio de-novo assembly
written by Ap1438 •
-
Statistics analysis of assembled genome from PacBio HiFi reads using Hifiasm
written by K •
-
Aligning PacBio hifiasm CCS to reference genome using pbmm2
written by K •
-
k-mer distribution to estimate the heterozygosity of my assembly
written by pablo
-
Using HiCanu assembler on PacBio Hifi reads
written by pablo
-
Improving PacBio Assembly with Illumina reads
written by pablo
-
How to perform quality check and assembly using pacbio sequel data?
written by lakhujanivijay
-
help to do genome assembly
written by walid.cbs •
-
Pacbio Ccs Vs Subreads Explained ?
written by curious.genome •
hifiasm doesn't give you an alignment. You used an assembler to create an assembly.
You're right, I edited my post.
Do you have an idea about my question?
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 ofsamtools idxstatsoutput of alignment data.