What input formats does Minimap2 support?

Minimap2 seamlessly works with gzip'd FASTA and FASTQ formats as input.

How do I save the index for faster mapping?

You can save the index with the option -d and replace the reference sequence file with the index file on the minimap2 command line.

Minimap2

Minimap2 | Find AI List

Overview

Minimap2 is a fast sequence alignment program designed for aligning DNA or mRNA sequences against a reference database. It excels at handling long, noisy reads generated by PacBio or Oxford Nanopore sequencing technologies, as well as short reads from Illumina platforms. The tool uses minimizers to index the reference genome, enabling efficient identification of potential alignment locations. It supports various alignment modes, including genomic read mapping, splice-aware alignment for RNA-seq data, assembly-to-assembly alignment, and finding overlaps between long reads. Minimap2's speed and accuracy make it suitable for large-scale genomic analyses, assembly polishing, and comparative genomics, providing biologically meaningful alignments ready for downstream analyses.

Common tasks

Sequence Alignment Read Mapping Overlap Detection

FAQ

View all

What is Minimap2?

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

What are the typical use cases for Minimap2?

Typical use cases include mapping PacBio or Oxford Nanopore genomic reads, finding overlaps between long reads, splice-aware alignment of RNA-seq reads, aligning Illumina reads, and assembly-to-assembly alignment.

How fast is Minimap2 compared to other aligners?

For ~10kb noisy reads sequences, Minimap2 is tens of times faster than mainstream long-read mappers. For >100bp Illumina short reads, Minimap2 is three times as fast as BWA-MEM and Bowtie2.

How do I install Minimap2?

You can acquire precompiled binaries from the release page or compile from the source code using make. Make sure you have a C compiler, GNU make, and zlib development files installed.

FAQ+