Statistics analysis of assembled genome from PacBio HiFi reads using Hifiasm
Hi,
I had consensus reads from a PacBio sequencing. I used the assembler hifiasm to create an assembly on these CCS. I got five .gfa files. I have transformed .gfa file to .fasta contigs using bandage and awk command.
What can be used to get more statistics on the assembly?
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Dave Carlson
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K •
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K •
2 answers
You can get N50/NG50 from https://github.com/lh3/calN50.
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Billy Rowell •
This py3 script will get you basic fasta stats: https://github.com/PacificBiosciences/pb-assembly/blob/master/scripts/get_asm_stats.py
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gconcepcion
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Quast and BUSCO would be my initial suggestions, but it really depends on what specific stats you're looking to compute.
bandage gave me N50, total length but I am particularly looking for coverage and depth of the assembly.
To get that, you should maps the reads back to the assembly (e.g., with minimap2 for long reads) and then use a tool like samtools or mosdepth to get the depth from the sam/bam file.