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: NGS

Estimating insert length quickly for a read pair

Insert length is the length of the sequence in between a pair of reads. Sequencers are supplied DNA samples in fragments of a known length and each end is sequenced (generally in a 5′ to 3′ direction from both ends). For example if you have a fragment of 2Kbp and your reads had an average […]

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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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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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Short read improvements to MacVector 11.1

The ability to produce de novo assemblies of short read data was introduced into MacVector & Assembler 11 and we’ve enhanced this in MacVector 11.1. Now Assembler stores and visualises metadata on the type of short read you have and also stores and deals with the quality data stored in a better way. Mixing your […]

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MacVector 11.1 is now released

MacVector 11.1 has just been released. You can check out the new features of this release on this blog post or a fuller list is available here. Existing customers can download and install it now. Although as usual you will be notified by MacVector’s online notifier in due course. We are pleased with this release […]

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Next Generation sequencing formats

As is common with the lack of standards seen with most emerging technologies there are many different and competing types of sequencing file formats for storage of short read or next generation sequencing data. All these formats try to solve the same question of storing an almost unprecedented amount of sequence data in a useable […]

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