minimap2





ALERT: minimap2.com is a phishing site. Please don't use anything from that website.

```sh

git clone https://github.com/lh3/minimap2

cd minimap2 && make

./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam

./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

./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+)

./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam # Nanopore Q20 genomic reads (v2.27+)

./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 # PacBio Kinnex/Iso-seq (RNA-seq)

./minimap2 -ax splice --junc-bed=anno.bed12 ref.fa query.fa > aln.sam # use annotated junctions

./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam # short-read RNA-seq (v2.29+)

./minimap2 -ax splice:sr -j anno.bed12 ref.fa r1.fq r2.fq > aln.sam

./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 ./minimap2.1

```

• [Getting Started](#started)
• [Users' Guide](#uguide)
• [Installation](#install)
• [General usage](#general)
• [Use cases](#cases)
• [Map long noisy genomic reads](#map-long-genomic)
• [Map long mRNA/cDNA reads](#map-long-splice)
• [Find overlaps between long reads](#long-overlap)
• [Map short genomic reads](#short-genomic)
• [Map short RNA-seq reads](#short-rna-seq)
• [Full genome/assembly alignment](#full-genome)
• [Advanced features](#advanced)
• [Working with >65535 CIGAR operations](#long-cigar)
• [The cs optional tag](#cs)
• [Working with the PAF format](#paftools)
• [Algorithm overview](#algo)
• [Getting help](#help)
• [Citing minimap2](#cite)
• [Developers' Guide](#dguide)
• [Limitations](#limit)

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA

sequences against a large reference database. Typical use cases include: (1)

mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2)

finding overlaps between long reads with error rate up to ~15%; (3)

splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads

against a reference genome; (4) aligning Illumina single- or paired-end reads;

(5) assembly-to-assembly alignment; (6) full-genome alignment between two

closely related species with divergence below ~15%.

For ~10kb noisy reads sequences, minimap2 is tens of times faster than

mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more

accurate on simulated long reads and produces biologically meaningful alignment

ready for downstream analyses. For >100bp Illumina short reads, minimap2 is

three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data.

Detailed evaluations are available from the [minimap2 paper][doi] or the

[preprint][preprint].

Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from

the [release page][release] with:

```sh

curl -L https://github.com/lh3/minimap2/releases/download/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar -jxvf -

./minimap2-2.30_x64-linux/minimap2

```

If you want to compile from the source, you need to have a C compiler, GNU make

and zlib development files installed. Then type make in the source code

directory to compile. If you see compilation errors, try make sse2only=1

to disable SSE4 code, which will make minimap2 slightly slower.

Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To

compile for 32 bit ARM architectures (such as ARMv7), use make arm_neon=1. To

compile for for 64 bit ARM architectures (such as ARMv8), use `make arm_neon=1

aarch64=1`.

Minimap2 can use [SIMD Everywhere (SIMDe)][simde] library for porting

implementation to the different SIMD instruction sets. To compile using SIMDe,

use make -f Makefile.simde. To compile for ARM CPUs, use Makefile.simde

with the ARM related command lines given above.