Is there any good GWAS software for the whole bacterial genomes? Input should be sam/bams, annotations, vcfs, in other words --- the outputs of alignment and variant calling and information belonging to the host (drug resistance status, clinical and laboratory parameters). Thx.
See these posts:
Software For Analysis Of Bacterial Genomics.
Tools To Calculate Average Coverage For A Bam File?
https://insidedna.me/tutorials/view/sam-files-processing-variants-calling-in-genomes
Some articles:
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295408/
Explaining microbial phenotypes on a genomic scale: GWAS for microbes
I found GWAMAR and eCAMBER, if you know a better choice, let me know, pls
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version 2.3.6
See this post, relatively old, but comprehensive.
Good Gwas Papers / Resources
I will look for some new approaches.
Some recent papers:
Finding the genetic changes in bacteria
http://modmedmicro.nsms.ox.ac.uk/finding-the-hidden-genetic-changes-in-bacteria/
Bacterial GWAS: not just gilding the lily
http://www.nature.com.sci-hub.cc/nrmicro/journal/v14/n7/full/nrmicro.2016.82.html
Comparative genomics as a tool to understand evolution and disease
http://genome.cshlp.org/content/23/7/1063.full
The advent of genome-wide association studies for bacteria
http://biorxiv.org/content/biorxiv/early/2015/03/22/016873.full.pdf
Explaining microbial phenotypes on a genomic scale: GWAS for microbes
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461095/
Tools for visualization and analysis of molecular networks, pathways, and -omics data
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295408/
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743258/