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update README

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chhylp123
2024-10-13 19:07:51 -04:00
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@@ -23,10 +23,10 @@ yak count -b37 -t16 -o pat.yak <(cat pat_1.fq.gz pat_2.fq.gz) <(cat pat_1.fq.gz
yak count -b37 -t16 -o mat.yak <(cat mat_1.fq.gz mat_2.fq.gz) <(cat mat_1.fq.gz mat_2.fq.gz) yak count -b37 -t16 -o mat.yak <(cat mat_1.fq.gz mat_2.fq.gz) <(cat mat_1.fq.gz mat_2.fq.gz)
hifiasm -o HG002.asm -t32 -1 pat.yak -2 mat.yak HG002-HiFi.fa.gz hifiasm -o HG002.asm -t32 -1 pat.yak -2 mat.yak HG002-HiFi.fa.gz
# Improve contiguity for diploid genome assembly by self-scaffolding # Improve contiguity for diploid genome assembly by self-scaffolding (`--dual-scaf`)
hifiasm -o HG002.asm --dual-scaf --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz hifiasm -o HG002.asm --dual-scaf --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz
# Preserve more telomeres for human genomes # Preserve more telomeres for human genomes (`--telo-m CCCTAA`)
hifiasm -o HG002.asm --telo-m CCCTAA --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz hifiasm -o HG002.asm --telo-m CCCTAA --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz
# Hybrid assembly with HiFi, ultralong and Hi-C reads # Hybrid assembly with HiFi, ultralong and Hi-C reads