minimap2
TLDR
Map long reads to reference
$ minimap2 -a [reference.fa] [reads.fq] > [aligned.sam]
Map with preset for ONT reads$ minimap2 -ax map-ont [reference.fa] [ont_reads.fq] > [aligned.sam]
Map PacBio HiFi reads$ minimap2 -ax map-hifi [reference.fa] [hifi.fq] > [aligned.sam]
Map short reads$ minimap2 -ax sr [reference.fa] [reads_1.fq] [reads_2.fq] > [aligned.sam]
Create index$ minimap2 -d [reference.mmi] [reference.fa]
Use multiple threads$ minimap2 -t [8] -ax map-ont [reference.fa] [reads.fq] > [aligned.sam]
SYNOPSIS
minimap2 [options] target [query...]
DESCRIPTION
minimap2 is a versatile sequence aligner for DNA and RNA sequences. It can align long reads from PacBio or Oxford Nanopore, short reads, and even whole assemblies.
minimap2 is extremely fast and memory-efficient, becoming the standard for long-read alignment.
PARAMETERS
-a
Output SAM format.-x preset
Preset (map-ont, map-pb, map-hifi, sr, asm5).-t threads
Number of threads.-d file
Save index to file.-o file
Output file.-k k
K-mer size.-w w
Minimizer window.
PRESETS
$ map-ont - ONT reads to reference
map-hifi - PacBio HiFi reads
map-pb - PacBio CLR reads
sr - Short reads
asm5 - Divergent assembly
splice - Long-read RNA-seq
map-hifi - PacBio HiFi reads
map-pb - PacBio CLR reads
sr - Short reads
asm5 - Divergent assembly
splice - Long-read RNA-seq
CAVEATS
Output is PAF by default; use -a for SAM. Index size depends on reference. Presets should match data type.
HISTORY
minimap2 was developed by Heng Li (author of BWA) and published in 2018 as a fast, accurate aligner for long reads.
