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Tag: assembler

  • What can MacVector do for my lab?

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    Chris
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    Here’s what MacVector can do for your lab. Comparing sequences Whatever type of alignment your sequence needs, there’s a tool in MacVector. CRISPR Indel Analysis: Identify insertions and deletions following CRISPR editing of a target. Compare Genomes: Compares two related annotated genomes to identify identical, similar and weakly similar features. Sequence assembly of NGS data…

  • Comparing multiple reference assemblies

    Comparing multiple reference assemblies

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    Chris
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    MacVector 17 has a greatly improved Assembly Projects manager, for better organization of multiple sequencing datasets, multiple references sequences and repeated jobs. Every time you run a new assembly job (either a reference assembly or de novo). A new job object is created in the Assembly Project window contains resulting contigs and any unaligned reads…

  • Balancing Velvet KMER and coverage

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    Chris
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    The 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…

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

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    Chris
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    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…

  • Assemble bacterial genomes in minutes on your Mac laptop

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    Chris
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    MacVector 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…

  • Simple Assembly of Sanger Sequencing Files with MacVector Assembler

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    Chris
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    Update: As of September 2024 Assembler will be added at no cost when you upgrade or renew maintenance. Contact Support if you have not yet been upgraded. With 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…

  • Assembling sequencing data with MacVector and Assembler

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    Chris
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    Update: As of September 2024 Assembler will be added at no cost when you upgrade or renew maintenance. Contact Support if you have not yet been upgraded. To assemble various types of sequencing reads, follow these steps. Then follow one of the following: To create a de novo assembly from Sanger reads To create a…

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

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    Chris
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    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…

  • RNASeq Expression Analysis with NGS data

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    Chris
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    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…

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

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    by

    Chris
    in ,

    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…