Assembling reads against a reference with Minimap2

Minimap2

Minimap2 is a long-read reference assembler. It can align long reads to one or more genomes. Whereas Bowtie2 excels at mapping "short reads" (500nt or less) to a reference, Minimap2 can handle very long reads - i.e. Oxford Nanopore or Pacific BioSciences reads. Additionally Minimap2 is significantly faster than Bowtie, even with short reads.

If you have the Assembler module, you can assemble noisy long-read data from Pacific Biosciences or Oxford Nanopore using the minimap2 algorithm. This is similar to Bowtie2 but can handle long reads whereas Bowtie2 is optimized for short (less than 500nt) reads.

To use minimap2

1. Create a new Assembly Project - FILE | NEW | ASSEMBLY PROJECT
2. Click on the Add Ref toolbar button to add one or more reference sequences.
3. Then click on the Add Reads toolbar button and select one or more NGS data files.
4. While not essential, it is usually also a good idea to double-click on the Status column of each read to let MacVector know exactly what type of data you are analyzing.
5. Click on the Assemble toolbar button and select minimap2 from the menu.
6. The simplest option is to choose one of the presets in the resulting dialog that will tune the assembly parameters for your specific type of data.

Note that minimap2 is also very good at assembling short read data and in some circumstances may out-perform Bowtie2.

Related Topics.

Assembler

Quick Start

Assemble reads against a reference sequence with Bowtie2.

Assemble reads against a reference sequence with Minimap2.

Viewing coverage data across a reference contig for example for RNASeq analysis

Short Read Assembly

Importing Fastq data