All assemblies are stored using the BAM file format. This is a binary file that stores each read and where and which consensus/contig/reference it is mapped against. It is a compressed version of the pure text SAM format. For some post assembly tasks it is necessary to do further processing on the BAM file. To […]
Velvet is a short read aligner that works very well on a wide variety of reads. Velvet excels at de novo assembly of sequencing reads from second and newer generation sequencers. In our latest release, MacVector 13, we’ve added Velvet to Assembler. This joins the existing tools, Phrap for Sanger sequencing reads and Bowtie for […]
There are two main steps to creating a reference assembly. Mapping your reads against your reference sequence and then analysing the alignment for variations. Knowing the depth of reads, or coverage, of an alignment is important for both of these stages. A low average depth of coverage means that you have less confidence in the […]
This is part of a series of posts about and leading up to the release of MacVector 12.5. With Assembler 12.5 our developers have come up with an affordable and straightforward solution for assembling and visualizing your NGS data. Generating sequencing data is cheaper than it has ever been, however, with this increase in data […]
Our latest version, MacVector 12.5, will be released on the 1st of December, 2011. There’s some great new features in this release with the addition of extra alignment algorithms, Muscle and T-coffee, to the Multiple Sequence Alignment analysis interface, as well as many interface enhancements and performance improvements. However, the most important new feature in […]
This is part of a series of posts about and leading up to the release of MacVector 12.5. Assembler has always made it easy to assemble your sequencing projects. It hides the complicated algorithms and provides a point and click interface to show you the results. With the release of MacVector 12.5 the range of […]