官網：

https://github.com/lh3/minimap2

https://github.com/lh3/minimap2/releases/tag/v2.17

Download and install:

wget https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2
tar -jxvf minimap2-2.17_x64-linux.tar.bz2
cd minimap2-2.17_x64-linux/
/home/software/minimap2/minimap2-2.17_x64-linux/minimap2

General usage

Without any options, minimap2 takes a reference database and a query sequence file as input and produce approximate mapping, without base-level alignment (i.e. no CIGAR), in the PAF format:

minimap2 ref.fa query.fq > approx-mapping.paf

You can ask minimap2 to generate CIGAR at the cg tag of PAF with:

minimap2 -c ref.fa query.fq > alignment.paf

or to output alignments in the SAM format:

minimap2 -a ref.fa query.fq > alignment.sam

Minimap2 seamlessly works with gzip'd FASTA and FASTQ formats as input. You don't need to convert between FASTA and FASTQ or decompress gzip'd files first.

For the human reference genome, minimap2 takes a few minutes to generate a minimizer index for the reference before mapping. To reduce indexing time, you can optionally save the index with option -d and replace the reference sequence file with the index file on the minimap2 command line:

minimap2 -d ref.mmi ref.fa                     # indexing
minimap2 -a ref.mmi reads.fq > alignment.sam   # alignment

Importantly, it should be noted that once you build the index, indexing parameters such as -k, -w, -H and -I can't be changed during mapping. If you are running minimap2 for different data types, you will probably need to keep multiple indexes generated with different parameters. This makes minimap2 different from BWA which always uses the same index regardless of query data types.

REF:

https://github.com/lh3/minimap2#install

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