From 722ab7cd21a7c2c2188391d9467fd6e779b5aa98 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Tue, 7 Apr 2015 09:05:42 +0100 Subject: [PATCH] Remove smalt, add bowtie2 --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1d473f4b..481f8731 100644 --- a/README.md +++ b/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/