Disclaimer: These software are almost obsolete. They really are! But we are using them to demonstrate the processes used in genomic algorithms. Also, if we tried to use the most modern software, they would change multiple times before the semester completed! We strongly encourage you to find better software if you plan to use assemblers and RNA-Seq in your own experiments. For a discussion of scientists using outdated software see this 2018 article Scientists Continue to Use Outdated Methods

Here’s a more recent article which coins the term “Software collapse”

Readings

• Great information about the Pete supercomputer can be found at the OSU HPCC Website
• Tons of information at the home site for the SPAdes assembler
• Info on the old but good Velvet assembler
• Soapdenovo2 is also an older assembler, but it’s easy to use and gets the point across.