Remove smalt, add bowtie2

README.md

@@ -11,10 +11,10 @@ Installation
 ------------
 
 ARIBA has the following dependencies, which need to be installed:
+  * [bowtie2] [Bowtie2] version >= 2.1.0
   * [cd-hit] [cdhit] version >= 4.6
   * [samtools and bcftools] [samtools]  version >= 1.2
   * [MUMmer] [mummer] version >= 3.23
-  * [SMALT] [smalt] version >= 0.7.4
   * Either [SPAdes] [spades] version >= 3.5.0 or [Velvet] [velvet] version >= 1.2.07
     (SPAdes is recommended)
 
@@ -44,12 +44,12 @@ Usage
 Please read the [ARIBA wiki page] [ARIBA wiki] for usage instructions.
 
 
+  [bowtie2]: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
   [cdhit]: http://weizhongli-lab.org/cd-hit/
   [ARIBA wiki]: https://github.com/sanger-pathogens/ariba/wiki
   [gapfiller]: http://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller
   [mummer]: http://mummer.sourceforge.net/
   [samtools]: http://www.htslib.org/
-  [smalt]: https://www.sanger.ac.uk/resources/software/smalt/
   [spades]: http://bioinf.spbau.ru/spades
   [sspace]: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
   [velvet]: http://www.ebi.ac.uk/~zerbino/velvet/