Dear All,
I need to analyse two acinetobacter genomes isolated from 2 different patients who were in the same ward on the same day.
We found similar Antibiotic resistance profile in both the isolates.
We have done WGS & submitted the reads to genbank.
I need help with regards to the SNP analysis for these isolates.
Can someone please suggest the right tool to be used for this analysis.
I don't know if it is the best program for your data, but I have used the "Mauve" program and outputted an SNP file (see http://darlinglab.org/mauve/user-guide/files.html for a description of the SNP file output). This program can cope with multiple whole genomes, so it should be able to handle two genomes without a problem.
Mauve is available from http://darlinglab.org/mauve/download.html for Windows, Linux or MacOS.
There are different comparative genomics tools and automatic pipeline to perform SNPs analysis, It depends by what you are looking for. You can find someone here: https://omictools.com/.
For my part, I love to use Snippy by Torsten Seemann (https://github.com/tseemann/snippy), one of the smartest Unix-based tool for SNPs detection and alignment. Please note that using Snippy you need a reference genome whereas with kSNP (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118258) the reference genome is not required. Good luck
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