Tag: assembler
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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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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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MacVectorTip: Filtering NGS Data to retrieve reads matching a known sequence
So you just got your NGS reads back from that sequencing experiment and, wow, what a HUGE amount of data. Wouldn’t it be easier to handle if you could pare that down to just the gene/plasmid/sequence(s) you are interested in? MacVector to the rescue as it can read and filter fast/q files, even if they…
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MacVectorTip: Use Bowtie to remove contaminating reads prior to NGS Assembly
MacVector with Assembler can use Velvet and/or SPAdes for fast and memory efficient de novo NGS assembly of modest sized genomes (typically up to 40 Mbp or so) even on a laptop. One common task is to assemble NGS data from BAC clones.However, one problem that often arises is that the BAC DNA preparations may…
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MacVectorTip: Context-sensitive Menus in MacVector
Although Apple are well known (notorious?) for always providing mice with only a single obvious button, in reality the Mac interface from early versions of MacOS all the way to macOS Big Sur, plus many Mac apps, have always used right click menus (or more accurately “context sensitive menus”) to provide extra functionality. MacVector is…
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MacVectorTip: Viewing genotype changes in Align to Reference assemblies
The latest releases of MacVector, MacVector 18.0.1 (Intel) and MacVector 18.1.1 (Intel and Apple Silicon) have some tweaks to the output of the SNPs tab in the Align to Reference assembly window. The genotypes of any SNP changes now follow a consistent standard, and short deletions are also reported. If the region containing the nucleotide…
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Working from home: An overview of assembling sequence data with MacVector and Assembler
Working from home Here’s a series of blog posts on the wide range of functionality in MacVector that you may never have used before. This is an overview of the many different sequence assembly tools within MacVector. The MacVector team used these tools to mine existing sequencing archives to assemble a new Pangolin SARS-CoV–2 genome. To…
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101 things you (maybe) didn’t know about MacVector: #52 – Data mining to identify and analyze pangolin CoV-2 analogs to the human COVID-19 virus
One of the most underrated features in MacVector is the Database | Align to Folder function. You can use this as a more sensitive version of a local BLAST search to find sequences in a “database” that match a query sequence. But in this case the “database” is simply a collection of your own sequences,…
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Importing BAM files into an Assembly Project
You can import BAM files, containing reads mapped against a reference sequence, into a MacVector Assembly Project. As well as the BAM file(s) you will also need the original reference sequence the reads were mapped against. FASTA is fine, but an annotated reference is better for visualisation. The tool needed is called ADD CONTIG. This…
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Gap closing and genome finishing tools in Align to Reference and Assembler.
Automated algorithms can only take you so far with genome assembly. The final steps involved in finishing a genome always need manual intervention. MacVector’s various assembly editors have many tools for helping finish genome sequencing projects. For example, closing gaps, extending reference sequences and even automatically circularizing contigs. If you select reads, then right click…