From 2de2ab096b8022b4b9277dc40785f883b8ce5e79 Mon Sep 17 00:00:00 2001 From: Kat Holt Date: Thu, 6 Feb 2014 17:50:22 +1100 Subject: [PATCH] updated for version 0.1.3 --- README.md | 55 +++++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 47 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 39ac024..2a7de8b 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,9 @@ STs and/or reference genes. +Current release - v0.1.3 - Feb 6, 2014 + + Dependencies: python (v2.7.5), scipy @@ -18,10 +21,21 @@ bowtie2 v2.1.0 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml SAMtools v0.1.18 https://sourceforge.net/projects/samtools/files/samtools/0.1.18/ (NOTE 0.1.19 DOES NOT WORK) +Updates in v0.1.3 + +- Fixed a bug that occurred while trying to type genes from a user-supplied database (see issue #5, thanks to Scott Long) + +- Fixed a bug in gene detection reporting - genes are now correctly reported by cluster, rather than by gene symbol (see issue #7) + +- Added maximum divergence option for reporting (--max_divergence), default is now to report only hits with <10% divergence from the database (see issue #8) + +- added parameter to pass to bowtie2 parameter '-u N' to stop mapping after the first N reads. Default behaviour remains to map all reads. However, for large read sets (e.g. >100x), extra reads do not help and merely increase the time taken for mapping and scoring, and you may want to limit to the first million reads (100x of a 2 Mbp genome) using '--stop_after 1000000'. + + Authors - Michael Inouye, Harriet Dashnow, Bernie Pope, Kathryn Holt (University of Melbourne) -How to cite - Please check back for news on the paper. In the meantime, please cite "SRST2 - Short Read Sequence Typing for Bacterial Pathogens, http://katholt.github.io/srst/" +How to cite - Please check back for news on the paper. In the meantime, please cite "SRST2 - Short Read Sequence Typing for Bacterial Pathogens, http://katholt.github.io/srst2/" Problems? - Email drkatholt@gmail.com. For updates, join the srst2 google group https://groups.google.com/forum/#!forum/srst2. @@ -30,19 +44,36 @@ Installation ==== 1 - Install dependencies first -2 - Download the zip or tarball at the top left of this page and unpack it +2 - Get and install the code + +Option 1: -3 - Install using pip (http://www.pip-installer.org/) or easy_install +Download the zip or tarball at the top left of this page and unpack it -You may need to use sudo to install centrally: +Then install using pip (http://www.pip-installer.org/) or easy_install. +You may need to use sudo to install centrally. pip install srst2-0.1.0-beta/ -OR +or easy_install srst2-0.1.0-beta/ -4 - Test that the programs are installed properly +Option 2: + +Clone the git repository: + + git clone https://github.com/katholt/srst2 + +and then install with pip: + + pip install srst2/ + +OR do both at once: + + sudo pip install git+https://github.com/katholt/srst2 + +3 - Test that the programs are installed properly srst2 --version @@ -159,8 +190,12 @@ optional arguments: --no_gene_details Switch OFF verbose reporting of gene typing --min_coverage MIN_COVERAGE - Percent coverage cutoff for gene reporting (default - 90) + Minimum %coverage cutoff for gene reporting + (default 90) + + --max_divergence MAX_DIVERGENCE + Maximum %divergence cutoff for gene reporting + (default 10) --min_depth MIN_DEPTH Minimum mean depth to flag as dubious allele call @@ -171,6 +206,10 @@ optional arguments: (default 2) --prob_err PROB_ERR Probability of sequencing error (default 0.01) + + --stop_after STOP_AFTER + Stop mapping after this number of reads have been + mapped (otherwise map all) --other OTHER Other arguments to pass to bowtie2