aglB-WGS-growth

Data and analysis of whole genome sequencing and growth of ∆aglB strain in Hbt. salinarum

Corresponds to the paper "N-glycosylation is required for archaellin transcription and translation, archaella assembly and cell motility in Halobacterium salinarum" by Marianna Zaretsky, Cynthia L. Darnell, Amy K. Schmid, and Jerry Eichler.

Dependencies

Click on the links below for downloads, documentation, and dependencies

Whole genome sequencing (WGS) dependencies

• Python v 2.7
• Anaconda
• FastQC for quality control.
• TrimGalore! for trimming adaptors.
• [breseq]v 0.32.1(http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/index.html) for read mapping and analysis of mutations.
  • breseq publication: Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151: 165–188.

Growth data calculation dependencies

• Rstudio v1.1.463 coding environment
• R packages
  • plyr v 0.7.8
  • tidyr v 0.8.2
  • dplyr v 0.7.8
  • tibble v 1.4.2
  • ggplot2 v 3.1.0
  • tinytex v 0.9
  • data.table v 1.12.0

Instructions

WGS

• Install dependencies
• Open Jupyter notebook "aglB_genome_sequencing.ipynb" in Anaconda navigator by clicking "root > open with Jupyter notebook"
• Run the notebook using the fastq data files in the data folder

Growth data

• Install dependencies using the command 'install.packages()'
• Open Rmd file
• Run the file using csv data and metadata files in the data folder
• Supplementary Table S2 (given here in the ~/data folder) from Zaretsky et al resulted from code up to line 83 in Rmd file.