De Novo Assembly
Velvet (1) joins the growing family of Sequencher plugins in version 5.1. Velvet is a well-known de novo assembler, it requires no reference sequence. Although we talk about Velvet, it actually consists of two programs. Velveth prepares your dataset while Velvetg performs the assembly steps utilizing a method called the de Bruijn graph. Velvetg builds the contigs, and will even attempt to scaffold contigs that don't quite come together on their own.
Velvet can perform de novo assembly with Multiplex ID data. Sequencher automatically divides the data by barcode into separate files (bins), then aligns them and places the results into separate results folders. The results then can be viewed in the Tablet browser. The consensus sequence from each contig will appear in your Project Window.
Velvet was written to run on the command line. Sequencher protects you from the command line by making it as simple as a few clicks to launch an assembly run. Power users and novices alike can still access the command line parameters to add or change parameters, we have put in a new GUI to let you access and harness those too.
If you would like to know more about Velvet and de novo assembly with NGS data, then take a look at the De Novo Assembly Tutorial.
(1)Velvet: algorithms for de novo short read assembly using de Bruijn graphs.D.R. Zerbino and E. Birney. Genome Research 18:821-829