From f50e4765756a5b4707fbce06ccd775cc5a4e40e6 Mon Sep 17 00:00:00 2001 From: Ryan Wick Date: Sat, 30 Jul 2016 15:14:00 +1000 Subject: [PATCH] Markdown formatting fixes --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e15ddc8..a034029 100644 --- a/README.md +++ b/README.md @@ -79,7 +79,7 @@ Dependencies: Updates in v0.2.0 -1. Some improvements to allele calling, particularly for Klebsiella MLST locus mdh, kindly contributed by @andreyto. Includes rejection of read alignments that are clipped on both ends (likely to be spurious) and minor bug fixes associated with depth calculations. +1. Some improvements to allele calling, particularly for Klebsiella MLST locus mdh, kindly contributed by [andreyto](https://github.com/andreyto). Includes rejection of read alignments that are clipped on both ends (likely to be spurious) and minor bug fixes associated with depth calculations. 2. Updated E. coli serotype database to remove duplicate sequences. 3. Added mcr-2 colistin resistance gene to `ARGannot.r1.fasta` resistance gene database. 4. A `--threads` option was added, which makes SRST2 call Bowtie and Samtools with their threading options. The resulting speed up is mostly due to the Bowtie mapping step which parallelises very well.