How to call heterozygotes in trace files or Assembly Projects

In our latest release, MacVector 18.5, we added a new tool to call heterozygotes in sequencing reads. The heterozygote analysis tool allows you to either view heterozygotes in Sanger trace files or to permanently change the basecalled sequence with an ambiguity representing the called heterozygote. The tool works on multiple trace files in the Assembly […]

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MacVector 18.5.1

We’ve just released a minor update, MacVector 18.5.1. Changes include: Further enhancements for importing Sequencher projects (.spf) including heavily edited assemblies. A new setting for always opening MacVector in “light” mode even when macOS switches to “dark” mode. Easier remote activation of standard licenses for larger sites. increased number of seats for serverless network licenses. […]

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MacVectorTip: Identifying, Selecting and Assembling NGS reads with a variant genotype

When analyzing/assembling/aligning NGS data, there are many scenarios where you might want to separate out the reads representing different genotypes or variant sequences. MacVector makes this very easy. Take a reference sequence and choose Analyze | Align to Reference. Now click the Add Seqs button and select and add your NGS data files. NOTE: if […]

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MacVectorTip: Trimming trace files by quality

Many of our users are familiar with the ability of Sequencher to semi-automatically trim poor quality sequences from the ends of Sanger ABI reads. Although it is generally not necessary to do this in MacVector because most of the algorithms can automatically handle poor quality data, there are times when it can be beneficial. So […]

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MacVectorTip: correctly flagging PacBio and Oxford Nanopore datasets for assembly by Flye

MacVector 17.5 introduced Flye for assembly of PacBio and Oxford Nanopore reads. Flye joins Phrap, Velvet and SPAdes for de novo sequence assembly using along with Bowtie2 and Align To Reference for reference assembly. Flye is an assembler algorithm tuned to assemble low quality long reads such as those produced by the new generation of […]

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MacVectorTip: quality score visualization in sequence assemblies.

Quality scoring of Assemblies and Align to Reference alignments can be visualized directly on the sequence. Residues can be shaded according to their quality scores. These can be displayed anywhere quality values are available, including de novo and reference assemblies in Assembler and Align to Reference alignments. A Shading toolbar button lets you turn on […]

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MacVectorTip: Assembling Fungal Genomes using SPAdes

MacVector with Assembler can assemble bacterial genomes in just minutes on quite modest hardware. Currently MacVector has four de novo assembly tools (SPAdes, Velvet, Flye and Phrap). But what of larger genomes? It is currently impractical to run de novo assemblies of Human genomes on a low cost Mac, though RNA-Seq analyses against the human […]

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MacVector 18.2 is out! …and ready for macOS Monterey

MacVector 18.2 Overview We are very pleased to announce that MacVector 18.2 is available to download. MacVector 18.2 is a Universal Binary that runs natively on both Apple Silicon and Intel Macs. It is fully supported on macOS Sierra (10.12) to macOS Monterey (12). New features: Align to Reference Enhancements The Align to Reference alignment algorithm […]

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MacVectorTip: Using the Align to Reference Shading and Trimming toolbar buttons

MacVector’s Align to Reference Editor and the Contig Editor in Assembly Projects have two useful functions for visualizing assemblies. The Shading button turns on background coloring of the residues in the upper pane, based on quality values (these can be from Sanger reads or from NGS reads). The scale ranges from a dark red for […]

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MacVectorTip: Identifying, Selecting and Assembling NGS reads with a variant genotype

When analyzing/assembling/aligning NGS data, there are many scenarios where you might want to separate out the reads representing different genotypes or variant sequences. MacVector makes this very easy. Take a reference sequence and choose Analyze->Align to Reference. Now click the Add Seqs button and select and add your NGS data files. NOTE: if your reference […]

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