Improved Align to Reference SNP Reporting The main application icon and window toolbar appearance have been updated to match the macOS Big Sur “look and feel”. However, in our hands, they still out-perform equivalent older Intel- based computers. Currently, all of the embedded 3rd party algorithms are included as Universal Binaries with the exception of SPAdes and Bowtie – these run under Rosetta2 emulation on Apple Silicon machines. Other than the ability to run natively on M1 processors, MacVector 18.1.1 is essentially identical to MacVector 18.0.1 with the exception that the embedded Python framework has been updated to version 3.9. MacVector 18.1 is a Universal Binary, meaning that it can run natively on both Intel and Apple Silicon Macintosh computers. MacVector 18.1 is a Universal Binary application that means it runs natively on Apple Silicon and Intel Macs. To reduce clutter in the Assembly Project window toolbar, all of the assembly algorithms have been consolidated into a single Assemble toolbar button with a dropdown menu. This functionality replaces the old Primer Converter utility which no longer runs on modern macOS systems. Open the file with TextEdit, select all the rows of text, Edit | Copy, switch to MacVector and select File | New From Clipboard. Then export the data (or Save As…) in Tab Separated Values format or Comma Separated Values format. First, prepare your data in an Excel or Numbers spreadsheet with three columns – “Name”, “Sequence”, “Comment”. You can now directly import primer data into a MacVector Primer Database (.nsub) file. Importing of Primer Databases in TSV or CSV Format So, if you see the button on the toolbar, click on it to see what additional options are available. To make the availability of these options more obvious, these views now contain a “hamburger” button (three parallel horizontal lines) that displays the same context sensitive menu when clicked on. Many of the views and windows in MacVector have context-sensitive menus available when you right-click (or -click) in them. This can clean up noisy assemblies where a low percentage of reads have extra residues inserted leading to a lot of gaps in the consensus sequence and a very cluttered display. There is a new Remove Gaps context-sensitive (right-click) menu option that deletes residues in reads that correspond to a gap in the consensus sequence. This does not apply to NGS reads where it is impractical to view potentially millions of reads in the Map tab. When aligning ABI chromatogram data, or plain sequences, the Map tab now graphically displays the “trimmed” regions at either end of the sequences making it far more obvious when there is only partial alignment between two sequences. In addition, the Sensitivity setting can now be lower due to the enhanced consecutive gap detection, which also speeds up calculations. The alignment algorithm has been further optimized for speed and is now 2–10 fold faster depending on the sequences being aligned. mRNA sequences versus a genome, you should still use the cDNA Alignment option which will also take splice site consensus sequences into account. However, if you are expecting introns when aligning e.g. Now 20–40 consecutive gaps, such as might appear in CRISPR experiments are handled with ease, depending on settings. Previously, for the standard alignment algorithm, more than 5 or 6 consecutive gaps in either reference or read would be poorly resolved. The Align to Reference alignment algorithm has been overhauled to do a much better job handling larger numbers of gaps in the alignment between a reference sequence and a read. It is supported on macOS Sierra (10.12) to macOS Monterey (12). MacVector 18.2 is a Universal Binary that runs natively on both Apple Silicon and Intel Macs.
0 Comments
Leave a Reply. |
Details
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |