Merge pull request #153 from ncsa/joshfactorial-patch-1

Update README.md

Author: joshfactorial

README.md

@@ -1,7 +1,8 @@
-# The NEAT Project v4.2
-Welcome to the NEAT project, the NExt-generation sequencing Analysis Toolkit, version 4.2. This release of NEAT includes several fixes and a little bit of restructuring. There is still lots of work to be done. See the [ChangeLog](ChangeLog.md) for notes. We have discarded the fasta file writing for now and removed that code. We may add that in as a feature in the future, if users call for it. We also removed GC bias for now. It severely complicated implementation, and had very few noticeable effects. After discussing with some people at the Illinois Institute for Genomic Biology, it sounded like GC bias may be a bit of a non-factor with improved chemistries. These will be reintroduced if needed/called for. 
+# The NEAT Project v4.2 - BETA
+Welcome to the NEAT project, the NExt-generation sequencing Analysis Toolkit, version 4.2. This beta release of NEAT 4.0 includes several fixes and a little bit of restructuring. There is still lots of work to be done. See the [ChangeLog](ChangeLog.md) for notes. We may add that in as a feature in the future, if users call for it. We also removed GC bias for now. It severely complicated implementation, and had very few noticeable effects. After discussing with some people at the Illinois Institute for Genomic Biology, it sounded like GC bias may be a bit of a non-factor with improved chemistries. NEAT 4.0 represents the direction we would like to move the code, but unfortunately we ran into several issues in production, notably the very long processing times, that make it unviable for general use. If you would like to try NEAT 4.0, please do! If you run into issues, please post them on our issues page.
 
-We are also working on redeveloping NEAT in Rust, a memory and thread safe language that will lend itself well to the way NEAT works, check that out here: https://github.com/ncsa/rusty-neat
+# NEAT 3.4 - Stable
+NEAT 3.4 under "releases" is the stable version of NEAT, most closely following the original NEAT genReads 2.0. NEAT 4.0 ran into several production problems, including very slow runtimes on larger genomes, so we have decided to switch back to NEAT 3.4 as the default release while we try to improve NEAT 4.0. If you are cloning the repo, you can checkout tag 3.4 `git checkout 3.4` within the NEAT repo. We are also working on redeveloping NEAT in Rust, a memory and thread safe language that will lend itself well to the way NEAT works, check that out here: https://github.com/ncsa/rusty-neat
 
 Stay tuned over the coming weeks for exciting updates to NEAT, and learn how to [contribute](CONTRIBUTING.md) yourself. If you'd like to use some of our code, no problem! Just review the [license](LICENSE.md), first.