三代pacbio hifi序列基因组组装与去冗余

1. bam2fasta -o xx.ccs.bam

2. hifiasm -o xjg04 -t 50 --hg-size 1.5g xjg.hifi.original.fa

3. minimap2 -x map-pb -t 16 -a Haplotype_ctg.fa xjg.hifi.original.fa --secondary=no > shb.sam

4.samtools view -bS -T Haplotype_ctg.fa shb.sam | samtools sort -@ 16 -m 2G -o shb.sort.bam -T tmp.ali

5. purge_haplotigs readhist -b shb.sort.bam -g Haplotype_ctg.fa -t 16

6. purge_haplotigs contigcov -i shb.sort.bam.gencov -l 5 -m 36 -h 57 -j 101

7.purge_haplotigs purge -g Haplotype_ctg.fa -c coverage_stats.csv -a 60 -t 8 -o purge_shb_60 -d -b shb.sort.bam

8.purge_haplotigs clip -p purge_Cl_70.fasta -h purge_Cl_70_haplotigs.fasta