MacVectorTip: Quality scoring of manual edits to your contigs.

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. The intensity of the shading of residues indicates […]

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MacVectorTip: Trimming by Quality in sequence assemblies

Many of our users may be 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. […]

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MacVectorTip: organizing assemblies and sequencing datasets with the Assembly Project manager.

MacVector’s Assembly Project manager helps you organize multiple sequencing datasets, multiple reference sequences and repeated assemblies. You can store multiple assembly jobs in a single Assembly Project and directly compare multiple runs of the same dataset to determine the best assembly parameters. You can also compare different sequencing datasets assembled against the same reference sequence […]

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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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Viewing and applying individual putative heterozygotes

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 project manager or the Align to Reference editor. You can also run it on a single trace file in the Single Trace Editor. But […]

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Automatic Assembly of Sub-projects with Phrap (Sub-Assemblies)

New to MacVector 18.6 is the ability to sort and assemble reads from different datasets into individual sub-projects. This functionality is located in the phrap parameters dialog. When enabled and configured appropriately for your dataset it will automatically break out the input reads into sub-projects to be assembled separately. A simple pattern-matching text box lets […]

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Importing Sequencher project files into MacVector

Assembler is a plugin for MacVector that provides comprehensive sequence assembly functionality. Assembler is fully integrated into MacVector and allows you to manage sequencing data with the familiar MacVector style. You can design primers directly on a contig or BLAST that contig to identify it. MacVector’s Assembly Project manager Like Sequencher, MacVector with Assembler has […]

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Sequence Assembly: What can Assembler do for my lab?

Assembler is fully integrated into MacVector and allows you to manage sequencing data with the familiar MacVector ease. de novo sequence assembly using Phrap, Velvet and SPAdes with Flye for PacBio and Oxford Nanopore. Reference Sequence Assembly: Map millions of reads against genomes, transcriptomes or other reference sequences using Bowtie2. Compare Genomes: Compare two related annotated […]

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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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