Question: Is there any good GWAS software for the whole bacterial genomes?
3
gravatar for hrenchert747
2.9 years ago by
hrenchert74750
hrenchert74750 wrote:

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.

gwas • 1.8k views
ADD COMMENTlink modified 2.8 years ago • written 2.9 years ago by hrenchert74750
0
gravatar for natasha.sernova
2.8 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

See these posts:

Software For Analysis Of Bacterial Genomics.

Bacterial GWAS analysis?

Is Bcbio-nextgen software good for the whole genome sequencing alignment and variant calling, are there any alternatives?

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

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743258/

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by natasha.sernova3.4k
0
gravatar for hrenchert747
2.8 years ago by
hrenchert74750
hrenchert74750 wrote:

I found GWAMAR and eCAMBER, if you know a better choice, let me know, pls

ADD COMMENTlink written 2.8 years ago by hrenchert74750

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/

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by natasha.sernova3.4k
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