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!

Tag Archives: bowtie

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 […]

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How Assembler uses quality scores to create assemblies

A common problem with all types of sequence assembly is distinguishing between sequencing errors and true genomic variations. Quality scores are one way to help the algorithm identify if a variation is of high quality and therefore likely to be a SNP or a sequencing error. For Assembler trace files can be basecalled with Phred, […]

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MacVector Talk: July 2014: Sequence assembly on the desktop with MacVector and Assembler.

Generating sequencing data is cheaper than it has ever been. However, with this increase in data has come a problem with easy analysis. Assembling 20 reads for your site directed mutagenesis project is easy. Why should dealing with 20 million reads of your bacterial genome be any harder? In our Summer newsletter we talk about […]

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Accessing BAM files from an Assembly Project file

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 […]

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de novo assembly with Velvet

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 […]

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Assembler: Using the coverage map of the Reference Contig editor to analyze your assembly

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 […]

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MacVector 12.5: Creating reference assemblies with Bowtie

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 […]

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MacVector 12.5: Get Assembler for half price!

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 […]

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MacVector 12.5: Sequence Assembly made easy.

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 […]

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