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

An overview of assembling sequencing data with MacVector’s Assembler plugin

To assemble various types of sequencing reads, follow these steps. Choose File | New | Assembly Project to create a new empty project file. Then follow one of the following: To create a de novo assembly from Sanger reads Click on the Add Reads tool bar button, then select the sequence files you wish to […]

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Import Multi-Sequence Genbank Files into an Assembly Project for easy access to Features

There are many genomes in the Genbank database that cannot be downloaded as single annotated sequences. These might be large multi-chromosome eukaryotic genomes, but, increasingly, partially sequenced bacterial chromosomes where the major contigs have been annotated using the NCBI annotation pipeline. Typically, when you encounter these, there are options to download annotated versions of these […]

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RNASeq Expression Analysis with NGS data

If you have the Assembler module, MacVector can align millions of NGS reads from RNASeq experiments against large genomes and generate a coverage table displaying the relative expression levels of every gene in a genome. The key to this functionality is that you must have a reference genome with genes annotated as CDS or gene […]

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Use a right-click in the Contig Editor tab to see if your contig can be circularized

MacVector 16 incorporates no less than THREE different de novo assemblers, phrap, velvet and SPAdes. While all are great assemblers, with each having their own specific advantages, none of them will generate a circular sequence from input reads. However, MacVector 16 also includes a new feature to help you with this. If you are assembling […]

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101 things you (maybe) didn’t know about MacVector: #51 – Rapid assembly of genomes with Velvet and SPAdes

Not so long ago, to assemble even a small genome with Next Generation Sequencing data required an array of clustered computers and a lot of patience. But improvements in algorithms and hardware mean that it is now realistic to assemble bacterial genomes, or even smaller eukaryotic genomes using MacVector on a modest laptop machine. MacVector […]

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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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Estimating insert length quickly for a read pair

[Edit┬áDecember 20, 2017 – As of MacVector 15.5 you can simply right click a READ and select “SEE MATCHING READS” to view the pair of reads. The total sequence length is selected. ] Insert length is the length of the sequence in between a pair of reads. Sequencers are supplied DNA samples in fragments of […]

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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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