Our latest release, MacVector 18.7, sees the addition of Minimap2 to Assembler’s sequencing toolkit. So if you have the Assembler module, you can now map noisy long-read data from Pacific Biosciences or Oxford Nanopore to one or more genomes. Minimap2 is a reference assembler similar to Bowtie2. But 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.
Assembling reads against a reference with Minimap2
- Create a new Assembly Project – File | New | Assembly Project
- Click on the Add Ref toolbar button to add one or more reference sequences.
- Then click on the Add Reads toolbar button and select one or more NGS data files.
- 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.
- Click on the Assemble toolbar button and select minimap2 from the menu.
- 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.
- Now run the alignment by clicking OK
MacVector 18.7 was released in July 2024 and introduces a History tab to track the construction of your expression vectors and clones. It also includes direct support for Codon Usage Tables, creating custom Codon Usage Tables and batch translation of CDS features. Additionally, MacVector 18.7 enhances Assembler’s toolkit by adding a new reference assembler for mapping PacBio and ONT sequencing reads to your reference sequences.