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MANUAL

@@ -19,8 +19,9 @@ Linux, and Solaris.
 [Bowtie] also forms the basis for other tools, including [TopHat]: a
 fast splice junction mapper for RNA-seq reads, [Cufflinks]: a tool for
 transcriptome assembly and isoform quantitiation from RNA-seq reads,
-and [Crossbow]: a cloud-computing software tool for large-scale
-reseuqncing data.
+[Crossbow]: a cloud-computing software tool for large-scale
+resequencing data,and [Myrna]: a cloud computing tool for calculating
+differential gene expression in large RNA-seq datasets.
 
 If you use [Bowtie] for your published research, please cite the
 [Bowtie paper].
@@ -32,6 +33,7 @@ If you use [Bowtie] for your published research, please cite the
 [TopHat]:          http://tophat.cbcb.umd.edu/
 [Cufflinks]:       http://cufflinks.cbcb.umd.edu/
 [Crossbow]:        http://bowtie-bio.sf.net/crossbow
+[Myrna]:           http://bowtie-bio.sf.net/myrna
 [Bowtie paper]:    http://genomebiology.com/2009/10/3/R25
 
 What isn't Bowtie?
@@ -1643,6 +1645,18 @@ format:
 
 Fields are separated by tabs.
 
+    -e/--ebwt-ref
+
+By default, when `bowtie-inspect` is run without `-s` or `-n`, it
+recreates the reference nucleotide sequences using the bit-encoded
+reference nucleotides kept in the `.3.ebwt` and `.4.ebwt` index files.
+When `-e/--ebwt-ref` is specified, `bowtie-inspect` recreates the
+reference sequences from the Burrows-Wheeler-transformed reference
+sequence in the `.1.ebwt` file instead.  The reference recreation
+process is much slower when `-e/--ebwt-ref` is specified.  Also, when
+`-e/--ebwt-ref` is specified and the index is in colorspace, the
+reference is printed in colors (A=blue, C=green, G=orange, T=red).
+
     -v/--verbose
 
 Print verbose output (for debugging).

doc/manual.html

@@ -4119,25 +4119,6 @@ <h1>Table of Contents</h1>
 >Use <code
   >&lt;int&gt;</code
   > as the seed for pseudo-random number generator.</p
-></td></tr><tr><td id="bowtie-build-options-old-reverse">
-<pre
-><code
-  >--old-reverse
-</code
-  ></pre
-></td><td>
-<p
-><code
-  >bowtie-build</code
-  > versions prior to 0.12.6 would construct the reverse index (in the <code
-  >.rev.1.ebwt</code
-  > and <code
-  >.rev.2.ebwt</code
-  >) by first reversing each unambiguous stretch of nucleotides then concatenating the reversed strings. Starting with <code
-  >bowtie-build</code
-  > 0.12.6, the reverse index is constructed by first concatenating the unambiguous stretches of nucleotides, then reversing the concatenated string. Specify <code
-  >--old-reverse</code
-  > to revert to the old behavior. Both types of index are fully forward and backward compatible, unless otherwise noted.</p
 ></td></tr><tr><td>
 <pre
 ><code