Minimap2 Fast DNA & RNA Sequence Aligner
Minimap2 is a state-of-the-art sequence alignment tool designed for aligning DNA or RNA sequences against large reference databases, such as genomes or transcriptomes. It is known for its speed, accuracy, and flexibility, making it suitable for handling both short reads (like from Illumina) and long reads (like from Oxford Nanopore or PacBio). Minimap2 can also perform spliced alignments, which makes it a great choice for RNA-Seq data analysis.
Key Features
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Efficient Alignment
Minimap2 is optimized to align millions of reads quickly using minimal system resources.It outperforms many traditional aligners.
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Support for Reads
It handles both long-read technologies like Oxford Nanopore/PacBio and short reads like Illumina.
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Spliced Alignment
Minimap2 can align RNA sequences that span introns by detecting splice junctions.This is essential for analyzing.
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Compatible with SAM/BAM Output
Minimap2 outputs alignments in the widely used SAM/BAM format.This ensures seamless integration with tools like SAMtools.
Installation
Minimap2 can be installed using three common methods: building from source, using precompiled binaries, or via package managers. Below are detailed instructions for each approach.
Install from Source
This method is ideal for users who prefer to build the latest version manually or need full control over the build process.
Clone the repository:
- git clone https://github.com/lh3/minimap2.git
- cd minimap2
Build the executable:
- make
Verify the installation:
- ./minimap2 –version
Dependencies:
- GCC (C compiler)
- make utility
- Unix-based system (Linux or macOS recommended)
Install Using Package Managers
This is the easiest and most user-friendly method, especially for those already using package managers like Conda or Homebrew.
Conda (via Bioconda):
- conda install -c bioconda minimap2
- Compatible with Linux and macOS
- Automatically handles all dependencies
Homebrew (macOS/Linux):
- brew install minimap2
- Works on macOS (Intel & Apple Silicon) and Linux
Linux Package Managers:
As of now, Minimap2 is not available in the default repositories of APT (Ubuntu/Debian) or YUM (CentOS/Fedora). In such cases, you can:
- Use Conda or Homebrew
- Or download and run the precompiled binary
| User Type | Recommended Method |
|---|---|
| Beginners | Conda / Homebrew |
| Developers | Build from Source |
| Quick Setup | Precompiled Binary |
Usage and Basic Commands
Minimap2 works through the command-line interface (CLI). You give it a reference genome and the sequencing reads you want to align, along with some optional flags to control the behavior.
Command-Line Syntax
minimap2 [options] <ref.fa> <reads.fq>
Explanation:
- minimap2: This is the executable file.
- [options]: Various flags or settings like read type, number of threads, etc.
- <ref.fa>: Reference genome in FASTA format (e.g., human genome).
- <reads.fq>: Your sequencing data (usually in FASTQ format).
- Important: Always make sure both files are in the correct format (FASTA or FASTQ).
Command-Line Syntax
minimap2 [options] <ref.fa> <reads.fq>
Explanation:
- minimap2: This is the executable file.
- [options]: Various flags or settings like read type, number of threads, etc.
- <ref.fa>: Reference genome in FASTA format (e.g., human genome).
- <reads.fq>: Your sequencing data (usually in FASTQ format).
- Important: Always make sure both files are in the correct format (FASTA or FASTQ).
Minimap2 Common Modes (Presets)
| Mode | Usage Description |
|---|---|
| map-ont | For Oxford Nanopore long reads. |
| map-pb | For PacBio long reads (HiFi or CLR). |
| splice | For spliced alignment, typically for RNA-Seq reads to a genome (includes intron handling). |
| asm5 / asm10 | For aligning assembled genomes to other genomes (low divergence). |
Example Commands
minimap2 -ax map-ont ref.fa reads.fq > aln.sam
- -a: Output in SAM format (recommended for most use cases).
- -x map-ont: Preset optimized for Oxford Nanopore reads.
- ref.fa: Your reference genome.
- reads.fq: Your nanopore or pacbio read file.
- aln.sam: Output file.
Align Short Reads
minimap2 -ax sr ref.fa reads.fq > aln.sam
- -x sr: Preset for short reads.
- Mostly used for fast mapping (though BWA or Bowtie2 may be better for high-accuracy short reads).
Align Transcriptome Data (RNA-Seq)
minimap2 -ax splice -uf -k14 ref.fa rna_reads.fq > aln.sam
- -x splice: For spliced alignment of RNA-Seq.
- -u: For unstranded RNA (you can change this for stranded RNA).
- -f: Forces full-length read alignment.
- -k14: Sets the minimizer k-mer size (14 is typical for RNA-Seq).
- Output will include introns (gaps) in alignments.
Use Cases of Minimap2
Minimap2 is a versatile aligner, widely used in genomics and transcriptomics. Below are its major real-world applications:
Genome Assembly Polishing
What it means:
After assembling a genome (e.g., using long reads from Oxford Nanopore or PacBio), the result may contain errors like insertions, deletions, or mismatches.
How Minimap2 helps:
- It maps raw reads back to the draft genome assembly.
- Tools like Racon or Pilon use these alignments to identify and correct errors.
- Improves the base-level accuracy of assemblies.
Example:
minimap2 -x map-ont assembly.fasta reads.fq > aln.sam
Structural Variant Calling
What it means:
Structural variants (SVs) are large changes in DNA like deletions, insertions, duplications, inversions, or translocations.
How Minimap2 helps:
- Aligns long reads to a reference genome.
- Since long reads can span SVs, the alignments clearly reveal structural changes.
- Tools like Sniffles or SVIM use Minimap2 output to detect SVs.
Benefit:
Much better for SVs than short-read aligners like BWA or Bowtie2.
Transcriptome Mapping
What it means:
- Transcriptome mapping involves aligning RNA-seq reads to a genome to study gene expression and splicing.
How Minimap2 helps:
- With the -x splice preset, Minimap2 supports spliced alignment, meaning it can map RNA reads that cross exon-intron boundaries.
- Works well with both long-read RNA-Seq (e.g., ONT direct RNA) and short-read data.
Example:
minimap2 -ax splice -uf -k14 ref_genome.fa rna_reads.fq > rna.sam
| Use Case | What Minimap2 Does | Commonly Paired Tools |
|---|---|---|
| Genome Assembly Polishing | Aligns reads to draft assemblies to fix errors | Racon, Medaka, Pilon |
| Structural Variant Calling | Detects large DNA changes via long-read alignment | Sniffles, SVIM |
| Transcriptome Mapping | Maps spliced RNA reads to genome | StringTie2, TALON, FLAIR |
| Genome Comparisons | Aligns entire genomes for evolutionary or structural study | DotPlot, SyRI, Assemblytics |
FAQ's
What is Minimap2?
Minimap2 is a fast and efficient sequence alignment tool used for mapping DNA or RNA reads to a reference genome.
Who developed Minimap2?
It was developed by Heng Li, a prominent bioinformatics researcher.
Is Minimap2 open-source?
Yes, it is open-source and licensed under the MIT License.
What are the main use cases of Minimap2?
Long-read alignment, short-read alignment, spliced RNA-Seq mapping, genome-to-genome alignment.
How do I install Minimap2 on Linux?
Clone the GitHub repository and run make in the directory, or use Conda/Homebrew.
Is Minimap2 available for Windows?
It is not officially supported on Windows but can be run via WSL (Windows Subsystem for Linux).
Can I install Minimap2 using Conda?
Yes, run: conda install -c bioconda minimap2
Does Minimap2 require dependencies?
It requires a C compiler like GCC or Clang to build from source, but no special libraries.
Is a graphical interface available for Minimap2?
No, Minimap2 is command-line based only.
What file formats does Minimap2 support?
Input: FASTA/FASTQ; Output: SAM/BAM (via piping with samtools).
How do I align Oxford Nanopore reads?
Use the map-ont preset:
minimap2 -ax map-ont ref.fasta reads.fq > output.sam
How do I align PacBio reads?
Use the map-pb preset:
minimap2 -ax map-pb ref.fasta reads.fq > output.sam
Can Minimap2 handle paired-end reads?
Yes, by providing both FASTQ files in the command.
How do I perform spliced alignment for RNA-Seq?
Use the splice preset:
minimap2 -ax splice ref.fa rna_reads.fq > aln.sam
Is Minimap2 faster than BWA or Bowtie2?
Yes, especially for long-read data and large genomes.
How much RAM does Minimap2 use?
It depends on the genome size and read length, but generally uses low to moderate memory.
Does Minimap2 support multithreading?
Yes, using the -t option (e.g., -t 8 for 8 threads).
Can I limit the number of secondary alignments?
Yes, with the -N option (e.g., -N 5 to limit to 5 secondary alignments).
Does Minimap2 support gapped alignments?
Yes, it supports both gapped and spliced alignments.
What does the -a flag do in Minimap2?
It outputs alignments in SAM format.
What is chaining in Minimap2?
Chaining is an internal process that helps identify the best regions of similarity before alignment.
Can I use Minimap2 for genome assembly polishing?
Yes, it’s commonly used with tools like Racon or Medaka for this purpose.
Can Minimap2 align whole genomes?
Yes, using asm5, asm10, or asm20 presets for genome-to-genome alignment.
Does Minimap2 detect structural variants?
Not directly, but it can generate alignments used by SV callers like Sniffles.
Is Minimap2 compatible with samtools?
Yes, it outputs in SAM format that samtools can process.
Can I use Minimap2 in bioinformatics pipelines?
Absolutely, it’s compatible with Snakemake, Nextflow, and shell scripts.
Does Minimap2 work with compressed FASTQ files?
No, it does not natively decompress .gz; use zcat or pigz with a pipe.
Can I visualize Minimap2 output?
Yes, convert SAM to BAM and view it with IGV or similar tools.
Schema
Minimap2 - Fast Versatile DNA & RNA Sequence Aligner
Minimap2 is a fast, versatile aligner for mapping long noisy reads, short reads, RNA-seq, or assemblies to large reference genomes. #Minimap2
Price: Free
Price Currency: $
Operating System: Windows, macOS, and Linux
Application Category: Software
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