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2020-04-12 20:46:54 -04:00
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.TH hifiasm 1 "22 Mar 2020" "hifiasm-0.3.0" "Bioinformatics tools"
.TH hifiasm 1 "12 Apr 2020" "hifiasm-0.4.0" "Bioinformatics tools"
.SH NAME
.PP
@@ -307,16 +307,4 @@ the ease of visualization. Hifiasm keeps corrected reads and overlaps in three
binary files such as it can regenerate assembly graphs from the binary files
without redoing error correction.
.PP
Note that different species need different assembly graphs. For homozygous genomes,
the primary assembly contig graph is the best choice.
For species with high heterozygous rate, different haplotypes can be fully separated.
It is important to remove small bubbles from the haplotype-resolved unitig graph. The
reason is that some small bubbles are caused by somatic mutations or noise in data,
which are not the real haplotype information. In this case, haplotype-resolved processed
unitig graph without small bubbles should be better.
For ordinary human genome, different haplotypes cannot be fully separated due to the low
heterozygous rate. There are many small bubbles including haplotype information,
which cannot be simply removed. Thus, it is necessary to use the haplotype-resolved raw
unitig graph.