Merge pull request #158 from ncsa/joshfactorial-patch-3

Update README.md

Author: joshfactorial

README.md

@@ -1,6 +1,9 @@
-# The NEAT Project v4.2 - BETA
+# The NEAT Project v4.3
 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.
 
+# NEAT v4.3
+If you would like to try our newest features in NEAT, we have now added a parallelization module that will allow you to run NEAT in a parrallel process that will split your chromosome up by contig or by blocks of sequence. This code still may have bugs, for which we apologize, but the more people who try it out, the more we can improve the software. If you need worry-free operation, then please try NEAT 3.4.
+
 # 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
 
@@ -417,4 +420,4 @@ neat vcf_compare
 Mappability track examples: https://github.com/zstephens/neat-repeat/tree/master/example_mappabilityTracks
 
 ### Note on Sensitive Patient Data
-ICGC's "Access Controlled Data" documentation can be found at <a href = https://docs.icgc.org/portal/access/ target="_blank">https://docs.icgc.org/portal/access/</a>. To have access to controlled germline data, a DACO must be submitted. Open tier data can be obtained without a DACO, but germline alleles that do not match the reference genome are masked and replaced with the reference allele. Controlled data includes unmasked germline alleles.
+ICGC's "Access Controlled Data" documentation can be found at <a href = https://docs.icgc.org/portal/access/ target="_blank">https://docs.icgc.org/portal/access/</a>. To have access to controlled germline data, a DACO must be submitted. Open tier data can be obtained without a DACO, but germline alleles that do not match the reference genome are masked and replaced with the reference allele. Controlled data includes unmasked germline alleles.