Pseudomonas veronii Tn-seq analysis of soil and liquid growth conditions

Readme file content

The files stored here contain the following material as supplementary and source data for the manuscript in submission

Fitness-conditional genes for soil adaptation in the bioaugmentation agent Pseudomonas veronii 1YdBTEX2

Marian Morales, Vladimir Sentchilo, Nicolas Carraro, Senka Causevic, Dominique Vuarambon & Jan R. van der Meer

Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland

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Folder Tn-seq
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This folder has the scripts, procedures, raw and intermediate data of the Pseudomonas veronii tn-seq libraries Lib1 and Lib2, at time 0 and incubated in liquid, sand or silt microcosms for up to 51 generations of growth.

Subfolders are organized to the steps in the analysis, from the initial experimental design, to the sequence mapping, read cleaning, normalization procedures, essentiality analysis, paired (liq-soil) analysis, gene group plots and the COG-KEGG category analysis.

Scripts are text-readable for MATLAB, vs 2021b; or BASH-UNIX slurm command line tools. Data files are either .mat (MATLAB readable) or .xlsx (for the major summary steps).

Individual procedures and steps are described in Word documents, which then point to scripts in the script folder, output and the data formats.

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Community diversity data
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This folder has the raw fastq- files of the sample reads of the T1 incubated sand or silt-Tn5 library replicates. Four replicates in total, two sequencing data sets which were combined.

Folder also has the meta data as to the sample descriptions, and the OTU-taxa output file from Qiime2 analysis.