From 9de668084fe7953688f4d4624993cd8d894ae10d Mon Sep 17 00:00:00 2001 From: Kat Holt Date: Tue, 15 Mar 2016 13:35:17 +1100 Subject: [PATCH] update list of changes --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a57b732..0a529ae 100644 --- a/README.md +++ b/README.md @@ -83,9 +83,11 @@ Dependencies: Updates in master branch, to be in next release -1. /data directory includes files for subtyping of the LEE pathogenicity island of E. coli, as per [Ingle et al, 2016, Nature Microbiology](http://www.nature.com/articles/nmicrobiol201510). [Instructions below](https://github.com/katholt/srst2#typing-the-lee-pathogenicity-island-of-E-coli) +1. /data directory includes files for subtyping of the LEE pathogenicity island of E. coli, as per [Ingle et al, 2016, Nature Microbiology](http://www.nature.com/articles/nmicrobiol201510). [Instructions below](https://github.com/katholt/srst2#typing-the-lee-pathogenicity-island-of-e-coli) -2. Fixed ARGannot.r1.fasta to include proper mcr1 DNA sequence +2. Resistance gene database updates: +- Fixed ARGannot.r1.fasta to include proper mcr1 DNA sequence. +- Added columns to the ARGannot_clustered80.csv table, to indicate classes of beta-lactamases included in the ARGannot.r1.fasta database according to the [NCBI beta-lactamase resource](http://www.ncbi.nlm.nih.gov/pathogens/beta-lactamase-data-resources/) (new location for the Lahey list). 3. Fixed some issues with handling of missing data (i.e. where there were no hits to MLST and/or no hits to genes) when compiling results into a table via --prev_output. This could result in misalignment of gene columns in previous versions.