Improvements to README

Author: Lenbok

README.md

@@ -6,12 +6,88 @@ This software is provided under the Real Time Genomics Ltd Software
 Licence Agreement for Academic Non-commercial Research Purposes
 only. See [LICENSE.txt](LICENSE.txt)
 
+## Introduction
+
+There are many software packages available for next-gen sequencing
+analysis, here are some of the reasons to use RTG:
+
+* Comprehensive, cohesive, fast, sensitive and accurate variant
+  calling pipeline from FASTQ through to high-quality variants.
+* Robust, easy to use, and well supported.
+* Fast and accurate alignment, supporting popular sequencing
+  technologies, including alignment of Complete Genomics Inc reads.
+* Automatic base-quality recalibration computed on-the-fly during
+  mapping and applied during variant calling.
+* Variant calling both simple SNPs and complex haplotypes,
+  automatically realigning when necessary.
+* Pedigree-aware pipeline, joint Bayesian calling of multiple samples
+  in pedigrees with varying degrees of relatedness, from unrelated,
+  trios, quads, larger families, multi-generation pedigrees.
+* Pedigree-aware joint calling automatically includes de novo
+  discovery, including specific confidence scoring that the variant is
+  de novo. Again, this includes information from larger families where
+  available, not just trios. Offspring variant calls are automatically
+  phased from inheritance.
+* Variant calling allows specification of population priors in either
+  from general population variants or those in previously called
+  samples.
+* Sex-aware pipeline, automatically mapping to the correct chromosomes
+  for the sex of the sample, performing diploid or haploid variant
+  calling as appropriate (including PAR regions).
+* Joint Bayesian somatic variant detection, including support for
+  contamination, and providing post-calling updated contamination
+  estimate. Supports site-specific somatic mutation priors that allow
+  databases such as dbSNP/COSMIC/etc to support the somatic calling.
+* Tools for Q/A and sample checking: coverage analysis, detect
+  chromosome abnormalities, sample mislabelling, incorrect pedigree.
+* Includes sophisticated variant comparison tools for benchmarking and
+  ROC analysis to guide variant scoring and filtering.
+* Fast and comprehensive metagenomic analysis pipelines.
+* Species frequency composition and abundance analysis, including
+  bounds estimates and confidence scores both at the species and
+  higher taxon levels.
+* Species reported using both tabular data reports and interactive
+  Krona HTML pie charts.
+* Contaminant filtering and sample similarity analysis.
+* Includes tools for building and managing species reference databases
+  that include taxonomic structure (prebuilt databases are also
+  available).
+* Search reads directly against protein databases for functional
+  analysis.
+* Reproducible results -- unlike many other tools, the results don't
+  change when you enable multi-threading or when you repeat the same
+  run twice.
+
+
+RTG Core is available pre-packaged directly from our
+[website](http://realtimegenomics.com/products/rtg-core/), or follow
+the instructions below to build from this repository.
+
+## Support
+
+A PDF user manual is included in the installation or can be
+[viewed online](installer/resources/core/RTGOperationsManual.pdf).
+
+You can use the commands in RTG Core to format your own reference
+datasets, or download common
+[pre-formatted references](http://realtimegenomics.com/news/pre-formatted-reference-datasets/)
+from our website.
+
+An
+[rtg-users](https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-users)
+discussion group is now available for general questions, tips, and
+other discussions.
+
+To be informed of new software releases, subscribe to the low-traffic
+[rtg-announce](https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-announce)
+group.
+
 If you require a license for commercial use or wish to purchase
 commercial support contact us via [email protected].
 
 ---
 
-## Prerequisites
+## Prerequisites for building from source
 
 * Java 1.7 or later
 * apache ant 1.9 or later
@@ -26,15 +102,15 @@ Core, so you must clone both repositories:
     $ cd rtg-core
 
 To update, you will need to perform a `git pull` on both
-repositories. Advanced users may use `git subtree` to have both RTG
+repositories.  Advanced users may use `git subtree` to have both RTG
 Tools and RTG Core within a single repository (it's what we use during
 development).
 
 ## Compile / run unit tests
 
     $ ant runalltests
 
-## Building RTG Core
+## Building RTG Core package
 
 To build the RTG Core Non-Commercial package which can be locally
 installed and run:
@@ -47,46 +123,17 @@ This will create an installation zip file under `dist`.
 
 Uncompress the installation zip:
 
-    $ cd /where/you/want/to/install/
+    $ cd /my/install/dir/
     $ unzip /path/to/rtg-core/dist/rtg-core-VERSION-nojre.zip
 
 Follow the instructions contained in the `README.txt`. This build will
 use the system Java by default, so ensure it is Java 1.7 or later.
 
-You can use the commands in RTG Core to format your own reference
-datasets, or download common
-[pre-formatted references](http://realtimegenomics.com/news/pre-formatted-reference-datasets/)
-from our website.
-
 For a nice demonstration of the features of RTG Core for sex and
 pedigree aware mapping and variant calling on data generated from
 scratch using the RTG Core simulation tools, run the `demo-family.sh`
 script contained in the scripts of the installation directory:
 
+    $ cd /my/install/dir/rtg-core-VERSION/
     $ ./scripts/demo-family.sh $PWD/rtg
 
-A PDF user manual is included in the installation directory or can be
-[viewed online](installer/resources/core/RTGOperationsManual.pdf).
-
-## Release history
-
-See [doc/ReleaseNotes.txt](doc/ReleaseNotes.txt) for full release
-history details.
-
-## Support
-
-An
-[rtg-users](https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-users)
-discussion group is now available for general questions, tips, and
-other discussions.
-
-To be informed of new software releases, subscribe to the low-traffic
-[rtg-announce](https://groups.google.com/a/realtimegenomics.com/forum/#!forum/rtg-announce)
-group.
-
-Some email support will be available via `[email protected]`
-which we will do our best to fulfill. If you have specific support or
-service requirements, talk to us about our support offerings which
-include guaranteed response times, training, project advice, priority
-bug fixes and feature requests.
-