minimap2安装及使用

#Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database.

#使用minimap2进行长reads比对，对于～10kb的noisy reads，minimap2的速度以及准确度更高（错误容忍度高达15%）

https://academic.oup.com/bioinformatics/article/34/18/3094/4994778

https://github.com/lh3/minimap2

一、简介
minimap2典型的用途包括：
（1）将TGS长reads比对到参考基因组；
（2）查找错误率高达15%的长reads之间的重叠；
（3）通过长reads发现可变剪切；
（4）对齐Illumina单端或成对端读取；
（5）Assembly与Assembly间比对；
（6）两个近缘种（差异在～15%以下）间的全基因组比对。

二、安装

conda install -c bioconda minimap2

三、使用

#比对长reads

minimap2 -t 48 -ax map-ont ref.fa input.ont.fa | samtools view -@ 48 -bS > ont.aln.bam
minimap2 -t 48 -ax map-pb ref.fa input.hifi.fa | samtools view -@ 48 -bS > hifi.aln.bam

#比对SE/PE短reads

minimap2 -ax sr ref.fa reads-se.fq > aln.sam
minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sam
minimap2 -ax sr ref.fa reads-interleaved.fq > aln.sam

#比对Assemblies（比对完后结果直接输入给http://assemblytics.com/进行结构变异分析），当然此处更常规的做法还是使用MUMmer+Assemblytics进行基因组间的比对以及发现结构变异。

minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf

#更多使用案例

# 长序列比对到ref
./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam
# 先创建index然后再map
./minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa
./minimap2 -a MT-human-ont.mmi test/MT-orang.fa > test.sam
# use presets (no test data)
./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam       # PacBio CLR genomic reads
./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam         # Oxford Nanopore genomic reads
./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19 or later)
./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam    # PacBio HiFi/CCS genomic reads (v2.18 or earlier)
./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam      # short genomic paired-end reads
./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam       # spliced long reads (strand unknown)
./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore Direct RNA-seq
./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam    # Final PacBio Iso-seq or traditional cDNA
./minimap2 -ax splice --junc-bed anno.bed12 ref.fa query.fa > aln.sam  # prioritize on annotated junctions
./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf             # intra-species asm-to-asm alignment
./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf     # PacBio read overlap
./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf    # Nanopore read overlap
# man page for detailed command line options minimap2