Tag: assembler

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

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    Chris
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    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…

  • Accessing BAM files from an Assembly Project file

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    Chris
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    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…

  • de novo assembly with Velvet

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    Chris
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    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…

  • Public beta of MacVector 13

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    Chris
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    There’s a public beta of our imminent release MacVector 13 ready for downloading and testing on our website. You just need an active license for MacVector 12.7 to run this. Watch out for the new easier way of installation (no installer, just drag to your Applications folder!). As well as a redesign of the interface…

  • 101 things you (maybe) didn’t know about MacVector: #18 – Aligning Chromatogram (ABI) Sequences

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    Kevin
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    I blogged about this a few years ago, but its something that still comes up on a regular basis. The blog link discusses the 6 main alignment algorithms in MacVector and how to decide which is the most appropriate for accomplishing different tasks. One common request we get is “I want to see my chromatograms/traces…

  • MacVector 12.5: Interface improvements and redesign

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    Chris
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    This is part of a series of posts about the shortly to be released MacVector 12.5. With each release of MacVector as well as adding new features we continually redesign and rewrite many existing parts of MacVector. This is done for a number of reasons. For example: to accommodate changes in OS X, where generally…

  • MacVector 12.5: Creating reference assemblies with Bowtie

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    Chris
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    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…

  • MacVector 12.5: Get Assembler for half price!

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    Chris
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    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…

  • MacVector 12.5: Sequence Assembly made easy.

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    Chris
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    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…

  • MacVector, Assembler and network licensing.

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    Chris
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    We recently changed the way that Assembler network licenses are shared out to make it easier for many users to share a single license. Previously an Assembler license was checked out whenever you loaded MacVector with Assembler.  However, now an Assembler license is only checked out when you start a new assembly project or open…