Update README.md

README.md

@@ -334,7 +334,7 @@ SRR5427886.10866    chr14:53438632,+                    SRR5427886.4746    singl
 * To avoid excessive memory usage and the imprecision inherent in floating-point values, a maximum of 10 alignments per read/fragment are analyzed by Genrich.  Reads/fragments with more than 10 alignments within the `-s` threshold are subsampled based on the best alignment scores; in the case of ties, alignments appearing first in the SAM/BAM are favored.
 * The alignment score for a fragment (pair of reads) is equal to the sum of the reads' individual scores.
 * Properly paired alignments take precedence over unpaired alignments, regardless of the alignment scores.
-* As stated [above](#multimap), [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml) reports secondary alignments in [`-k <int>` mode](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#k-mode-search-for-one-or-more-alignments-report-each) or [`-a` mode](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#a-mode-search-for-and-report-all-alignments).  Note that a [software bug](https://github.com/BenLangmead/bowtie2/issues/202) causes errors with some secondary alignments that Bowtie2 reports; perhaps it will be fixed at some point.  The short read aligner [BWA](http://bio-bwa.sourceforge.net/bwa.shtml) does not report secondary alignments.
+* As stated [above](#multimap), [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml) reports secondary alignments in [`-k <int>` mode](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#k-mode-search-for-one-or-more-alignments-report-each) or [`-a` mode](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#a-mode-search-for-and-report-all-alignments).  The short read aligner [BWA](http://bio-bwa.sourceforge.net/bwa.shtml) does not report secondary alignments.
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 ### Unpaired alignments<a name="unpaired"></a>