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: velvet

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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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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