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How to split large fastq files for more manageable assemblies
Read more: How to split large fastq files for more manageable assembliesWe’ve previously discussed how important it can be to make sure you are using the appropriate number of fastq reads from an NGS experiment to ensure you obtain the results you are looking for. Using too many reads can confuse algorithms with the massive coverage increasing mis-assemblies due to background errors in the reads. In…
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Balancing Velvet KMER and coverage
Read more: Balancing Velvet KMER and coverageThe Velvet assembly algorithm in MacVector is blazingly fast and generates excellent assemblies. However, you do have to be careful when assembling NGS data to be sure that the parameters you submit are appropriate for the data you are assembling in order to get optimal results. By far the most important parameter is the KMER…
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Use a right-click in the Editor tab to see if your contig can be circularized
Read more: Use a right-click in the Editor tab to see if your contig can be circularizedMacVector 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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Getting Started with MacVector
Read more: Getting Started with MacVectorAny molecular biologist should be able to start getting useful results within an hour of starting to use MacVector by just exploring the toolbar and menus. Everything is logically named to be obvious. However, there’s still a lot of functionality that a user will never know exists. That is unless you read the manual or…
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The MacVector Team are at ASM Microbe 2018 in Atlanta this week.
Read more: The MacVector Team are at ASM Microbe 2018 in Atlanta this week.We’re at ASM Microbe 2018 in Atlanta from Friday until Sunday (8–10th June). The exhibit hall hours are again different from the last two years. Friday, June 8th – 10:30 AM – 5:00 PM Sat. June 9th – 10:30 AM – 5:00 PM Sunday, June 10th – 10:00 AM – 4:00 PM We’re on booth…
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Workflows on designing, testing and storing primers in MacVector
Read more: Workflows on designing, testing and storing primers in MacVectorMacVector is the best PCR Primer design application on macOS. It has many innovative primer tools to make designing, analyzing and cataloging your primers or oligos easy. Here are a few typical workflows. Designing primers Amplifying a gene You can design a set of primers to amplify a gene in as little as three mouse…
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MacVector 16 and macOS High Sierra 10.13.4.
Read more: MacVector 16 and macOS High Sierra 10.13.4.Apple have just released macOS® High Sierra 10.13.4. This may appear to be just an incremental update to macOS High Sierra. However, under the hood there are some major changes, not least is a new warning dialog if you are running an older application on macOS High Sierra. With the release of macOS High Sierra 10.13.4…
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Assemble bacterial genomes in minutes on your Mac laptop
Read more: Assemble bacterial genomes in minutes on your Mac laptopMacVector with Assembler contains some remarkably powerful algorithms for assembling Next Generation Sequencing (NGS) data. Not so long ago, you needed a powerful Linux server with lots of memory for de novo assembly of whole genomes. But with advances in the efficiency of algorithms and improvements in hardware, it is now possible to assemble quite…
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Simple Assembly of Sanger Sequencing Files with MacVector Assembler
Read more: Simple Assembly of Sanger Sequencing Files with MacVector AssemblerWith MacVector Assembler, assembling ABI Sanger Sequencing files is simple, fast and accurate. MacVector uses the popular phred/phrap/cross_match set of tools from the University of Washington. To improve accuracy, and to help resolve repeats, these tools use “quality scores” (popularly known as “phred scores”), giving them an advantage over many other methods. To assemble two…
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Assembling sequencing data with MacVector and Assembler
Read more: Assembling sequencing data with MacVector and AssemblerMacVector has a software plugin called Assembler that integrates directly into the DNA sequence analysis toolkit and provides DNA sequence assembly functionality. Dealing with sequencing reads has never been easier. MacVector includes no less than five different assemblers just a few mouse clicks away from your sequencing reads. Phrap assembles Sanger sequencing reads or existing…
