Merge branch 'master' into test-devel

diff --git a/README b/README
index 4095239..004e8c2 100644
--- a/README
+++ b/README
@@ -25,6 +25,8 @@ of ChIP-Seq data and has been applied to the organism Tetrahymena thermophila.
   - Downloading datasets
   - Comparing RACS results to MACS

+* Performance & Parallelism
+
 * Notes about the use of RAMdisk and storage space as "working space"

 * Examples
@@ -117,7 +119,7 @@ a internet connection!) and type:
 that should clone (download and copy) the latest version of our pipeline in your computer,
 creating a directory called "RACS", containing the following files and sub-directories:

-``
+```
 RACS
  ├── AUTHORS
  ├── CITATION
@@ -161,7 +163,7 @@ RACS
      └── racs_monitor.sh
      └── setup.R
      └── compare.R
-''
+```


 Updating RACS:
@@ -428,6 +430,27 @@ More concrete examples and uses are presented in the examples section below.

 -------------------------------------------------------------------------------

+* Performance & Parallelism
+
+RACS can utilize multi-core (threading) parallelism for its ORF pipeline.
+This is achieved through the multi-threaded features of BWA.
+A performance and scaling analysis plot is included in the "doc" subdirectory
+of this repository -- see  doc/RACS_scaling.pdf  or  doc/RACS_Scaling.html (this
+last file is an HTML file that can be opened with any browser and will display a
+3D visualization of the scaling analysis with interactive features).
+
+We should also notice that in some cases, depending on the size of the data and
+hardware specifications (ie. number of cores) where the pipeline is executed,
+results could slightly differ depending on how many cores/threads are used.
+Thisi, as disclaimed by BWA developers, is a characteristic of BWA (see
+https://github.com/lh3/bwa/issues/121 ).
+In our analyzes we discovered that this can occur, when using a number of
+threads larger than the actual number of physical cores in the computer (a
+typical technique known as hyper-threading).
+Nevertheless, this is an issue that users should be aware of, although our analysis
+showed that the variations are not statistically significant.
+
+
 * Notes about the use of RAMdisk and storage space as "working space"

 When using the main script for counting reads, the user has the ability of
@@ -465,7 +488,7 @@ Ie. a value of 8, means 8 times the original size of the initial data.
 The horizontal axis is runtime in seconds, and the '*' represents data points
 showing the trend in use of working space.

-
+```
   9 +-+---------+-----------+-----------+----------+-----------+---------+-+
     +           +           +           +          +           +           +
   8 +-+                                            ****                  +-+
@@ -487,7 +510,7 @@ showing the trend in use of working space.
     *           +           +           +          +           + *         +
   0 *-+---------+-----------+-----------+----------+-----------+-**------+-+
     0          500         1000        1500       2000        2500        3000
-
+```

 -------------------------------------------------------------------------------