Comments (1)
It would be better to not run purge_dups for the Hi-C phased assemblies. K-mer evaluation often underestimate the genome size.
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Related Issues (20)
- Question regarding quality threshold for PacBio and ONT assembly
- different size for diploid organisms with low heterozygosity levels
- Bus error problem
- Use p_ctg.fa and a_ctg.fa to fill the gaps of hap1.fa and hap2.fa?
- Telo option
- Clarification on hifiasm (HiC)
- Clarification on the post-join step
- How to replace a consensus reference with either haplotypes after asm?
- het peak -1 and second peak on kmer distribution plot missing HOT 3
- How to deal with extremely high mapping rate?
- How to deal with extremely high mapping rate? HOT 3
- hifiasm log file
- How to further improve the busco completeness?
- large and discontinuous assembly results using only HiFi sequencing data
- Change ptg*****l to ptg*****L.
- KMer Count is very skewed towards the beginning
- Discard the output file reads *.ec.fa
- a third of the hifi reads not present in gfa
- Missing and Duplicated Buscos in diploid haplotype-resolved assemblies
- Tetraploid with high heterozygosity
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