We’ve previously discussed how important it can be to make sure you are using the appropriate number of fastq reads from an NGS experiment to ensure you obtain the results you are looking for. Using too many reads can confuse algorithms with the massive coverage increasing mis-assemblies due to background errors in the reads. In […]
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 […]
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 […]
MacVector has a software plugin called Assembler that integrates directly into the DNA sequence analysis toolkit and provides DNA sequence assembly functionality. Dealing with sequencing reads has never been easier. MacVector includes no less than five different assemblers just a few mouse clicks away from your sequencing reads. Phrap assembles Sanger sequencing reads or existing […]
Not so long ago, to assemble even a small genome with Next Generation Sequencing data required an array of clustered computers and a lot of patience. But improvements in algorithms and hardware mean that it is now realistic to assemble bacterial genomes, or even smaller eukaryotic genomes using MacVector on a modest laptop machine. MacVector […]
Generating sequencing data is cheaper than it has ever been. However, with this increase in data has come a problem with easy analysis. Assembling 20 reads for your site directed mutagenesis project is easy. Why should dealing with 20 million reads of your bacterial genome be any harder? In our Summer newsletter we talk about […]
All assemblies are stored using the BAM file format. This is a binary file that stores each read and where and which consensus/contig/reference it is mapped against. It is a compressed version of the pure text SAM format. For some post assembly tasks it is necessary to do further processing on the BAM file. To […]
Velvet is a short read aligner that works very well on a wide variety of reads. Velvet excels at de novo assembly of sequencing reads from second and newer generation sequencers. In our latest release, MacVector 13, we’ve added Velvet to Assembler. This joins the existing tools, Phrap for Sanger sequencing reads and Bowtie for […]