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GcoGSA-BA Manual

Global core Genome SNP Analysis for Bacillus anthracis

Overview

Global core Genome SNP Analysis for Bacillus anthracis (GcoGSA) is a web service designed to detect SNPs and inferr phylogenetic positions among Bacillus cereus group species including B. anthracis species using NGS samples. GcoGSA-BA can also detect the existence of anthrax plasmids pXO1, pXO2, and three anthrax toxin proteins: LF, EF, and PA in the pXO1.

NGS: next-generation sequencing; SNP: single nucleotide polymorphisms; LF: lethal factor; EF: edema factor; PA: protective antigen;

GcoGSA performs:

Submitting query

  1. Change number of samples if more than 5 data set were to submitt. GcoGSA can accept upto 10 data sets at once.
  2. Input the project name, otherwise analysis ID will be automatically filled.
  3. Input strain name and select read files for each dataset.
    GcoGSA can accept:
    • gz compressed fastq formatted sequences (.fastq.gz) only.
    • either single ended or paired ended reads.
    • upto 2GBytes of data in total.
  4. Push "Send" button to submit the analysis.
  5. An e-mail will be sent after finished the analysis if e-mail address were input and the "Send an e-mail after finished analyzing." checkbox were checked.

Fig. 1. Submittion page.

Retrieving result

NOTICE: The analysis result will be deleted after 7 days.

Analysis results are shown in the main window.
Those chromosomes/plasmids/regions which have low coverage will be shown in gray, low read depth will be shown in dark blue.
SNPs in tabular and multifasta format, NJ phylogenetic tree in Newick and PDF format are available from the links.
All the results can be downloaded at once as a zip file from the "Download All" button.

NJ: Neighbor-joining


Fig. 2. Analysis result. Submitted data are Ames Ancestor, B. anthracis A0149, B. cereus G9241, and B. cereus VD166.
Two NJ phylogenetic trees will be shown for user convenience. One is the overview among the Bacillus celeus group species prepared in this server. The submitted samples will be shown in red. The other is the zoom up version that contain all the samples submitted.
For more precise analysis users can analyze the data using the SNPs data in either tabular or multifasta format.

Fig.3 Phylogenetic tree. Submitted data are Ames ancestor and Vollum.

Tips


Fig. 3. Results with warnings.

Troubleshootings

Problem: Analysis does not finish.
How to cite GcoGSA?
Other problems.