Minimap2 for mapping reads to genomes


Minimap2 is a fast general-purpose alignment program to map DNA and long mRNA sequences against a large reference database. It can be used for:


Minimap2 parameters

Read group parameters


Minimap2 aligner can be used for several different alignment and mapping tasks, including mapping of read sets containing very long reads (e.g. PacBio or Oxford nanopore reads). The Minimap2 tool in Chipster is intended only for single-end type mapping tasks where all the reads are in one input file. The reads can be in FASTQ or FASTA format.

The reference sequence set can be defined in two ways. 1) If only one input file is defined, then the reference genome is given with the Genome parameter that lists the genomes available in Chipster. 2) Alternatively, you can give the genome as a second input file in fasta format. If the reference sequence file is provided by the user, then the value of the Genome parameter is ignored.

User must always select a task type from the task menu. Assigning a task type takes in use a predefined set of minimap2 parameters that are optimal for a specific analysis task. The predefined task types include:
TaskMimimap2 parameters used
Map PacBio subreads to a genome-ax map-pb
Map Oxford nanopore reads to a genome-ax map-ont
Map PacBio Iso-seq or traditional cDNA to reference-ax splice -uf
Map Nanopore 2D cDNA-seq data to reference-ax splice
Map Nanopore Direct RNA-seq to reference-ax splice -uf -k14
Mapping against SIRV control reference-ax splice --splice-flank=no
Aligning assembly to reference genome-ax asm5
As there is no obvious default analysis for Minimap2, the task type does not have any default value. Instead this value must be defined by the user for each Minimap2 task.



This tool uses the Minimap2 aligner. Please cite the article:

  • Heng Li: Minimap2: pairwise alignment for nucleotide sequences
  • Please see the Minimap2 manual for more details.