General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Reference assembly with MacVector and Assembler

MacVector has a plugin module called Assembler that integrates directly into the main package and provides sequence assembly functionality. Assembler was designed from the ground up to be easy to use and allow users to easily manage the large amount of data that sequencing generates nowadays.

The Assembler interface is built around the Assembly Project window which gives great control over managing your reads and gives you easy access many different assembly tools. To bring data in you just drag and drop it from Finder into a new Assembly Project window.

Assembler uses many popular third party tools/algorithms that are widely respected and published.

De Novo assembly

  • Velvet
  • Phred/Phrap.
  • SPAdes

Reference Assembly

  • Bowtie2

Assembler also uses many other popular tools for variant calling. Assemblies are stored in the BAM file format which is the most widely used format. That means your data is not locked away in a proprietary format.

Assembler accepts reference sequences in many different formats (since it’s integrated within MacVector itself it’s trivial to directly download fully annotated references from the NCBI’s Genbank database).

Sequencing reads must be in FASTQ format. Although Assembler will import already assembled reads in BAM format.

The best way to try Assembler is to try it out. Download a 21 day trial version.

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