TANGENT!: Comparison Charts for NGS Platforms 2013

If you are thinking about buying an NGS platform...

Travis Glenn has released the 2013 tables comparing NGS platforms seven ways from Sunday, so you can make an informed decision.

I found them on a blog I follow: www.molecularecologist.com

Table 1a-c: de novo, resequencing and other applications. NGS Platform grades.

Table 2a: Runtime, reads and yield

Table 2b: Costs/run, Costs/MB, minimum costs

Table 3a: Instrument Costs

Table 3b: Computation Resources

Table 3c: Error Rates

Table 4: Advantages and disadvantages of each instrument

Citation: Glenn, TC. 2011. Field Guide to Next Generation DNA Sequencers. Molecular Ecology Resources. doi: 10.1111/j.1755-0998.2011.03024.x

Blog Series: WoG: Cesky Krumlov; Day 4: Assembly

Dr. Rayan Chikhi

Pennsylvania State University

Topic: De novo Assembly

A whole day of assembly!

There is no single program right now that is considered 'the assembler'. Different assemblers have advantages and disadvantages as well as things they are generally useful and not useful for. So one thing in todays assemblers is that they all take a lot of time and memory to run--especially when doing de novo assembly. One of the exceptions is the program Minia, developed by Dr. Chikhi which was designed to run efficiently using low memory requirement.

One of the important things that you need to know for assembly is what a k-mer is. A k-mer is any sequences with length k.

AGC is a k-mer with k=3

AGCT is a k-mer with k=4

AGCTT is a k-mer with k=5

You hopefully get the idea. 

There are two essential methods that assemblers use to assemble: de Bruijn graphs and overlap/string graphs. Now we sort of covered this in the Assembly prep blog...lets see if I can explain this better here now...