minimap比对

参考：[GitHub - lh3/minimap2: A versatile pairwise aligner for genomic and sload/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.24_x64-linux/minimap2
方法1
（1）：index

minimap2 -d ref.mmi R64.fna         

-d FILE: dump index to FILE []
生成索引文件ref.mmi
（2）alignment

nohup minimap2 -a ref.mmi ~/WGS/SY14/pacbio/fastq1/SRR6823435.fastq.gz > alignment1.sam 

在minimap2命令行中用索引文件替换引用序列文件
方法2

nohup minimap2 -ax map-pb R64.fna ~/WGS/SY14/pacbio/fastq1/SRR6823435.fastq.gz > alignment2.sam 

参数设置：
-a: output in the SAM format (PAF by default)
-x STR: preset (always applied before other options; see minimap2.1 for details) []
- map-pb/map-ont - PacBio CLR/Nanopore vs reference mapping
- map-hifi - PacBio HiFi reads vs reference mapping