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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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How do I evaluate my genome? #150

Open ld9866 opened 3 years ago

ld9866 commented 3 years ago

Hello, I have successfully completed the assembly, but now I want to evaluate the quality of the genome assembly. The software I want to use at present is Busco. But how do I convert this GFA format file for further analysis?
NA12878.asm.ec.bin NA12878.asm.hic.hap1.p_ctg.g NA12878.asm.hic.hap1.p_ctg.lowQ.be NA12878.asm.hic.hap1.p_ctg.noseq.gfa NA12878.asm.hic.hap2.p_ctg.g NA12878.asm.hic.hap2.p_ctg.lowQ.be NA12878.asm.hic.hap2.p_ctg.noseq.gfa NA12878.asm.hic.lk.bin NA12878.asm.hic.r_utg.gf NA12878.asm.hic.r_utg.lowQ.be NA12878.asm.hic.r_utg.noseq.gfa NA12878.asm.hic.tlb.bin NA12878.asm.ovlp.reverse.bin NA12878.asm.ovlp.source.bin

ld9866 commented 3 years ago

I used the following code, do not know if this is correct? awk '$1 ~/S/ {print ">"$2"\n"$3}' reads.gfa > reads.fasta

ptrebert commented 3 years ago

The line below is given in the README (see point "Getting started") of this repository to go from GFA to FASTA...

awk '/^S/{print ">"$2;print $3}' test.p_ctg.gfa > test.p_ctg.fa  # get primary contigs in FASTA
ld9866 commented 3 years ago

Thank you very much for your reply. I want to ask one more question, how do I evaluate the effectiveness of our genome assembly? At present, I want to use Busco, but I find this software very difficult to use. Is there any other method or script for this?

ld9866 commented 3 years ago

Thank you very much for your reply. I want to ask one more question, how do I evaluate the effectiveness of our genome assembly? At present, I want to use Busco, but I find this software very difficult to use. Is there any other method or script for this?

chhylp123 commented 3 years ago

Probably Hi-C is useful to evaluate completeness and misassemblies.

ptrebert commented 3 years ago

Mercury is also quite popular for assembly evaluation: https://github.com/marbl/merqury