Genome-centric analysis of gene transcription in microbial communities from biological soil crusts of the Negev Desert (Avdat Long-term Ecological Research Site)

This repository contains scripts used to process the metatranscriptomic data obtained from a rehydration and desiccation timeseries of biological soil crusts from the Avdat LTER site (N 30°36'33", E 34°44'48") in the Negev Desert, Israel. The results and discussion of the analysis are subject of the manuscript "Survival and rapid resuscitation permit limited productivity in desert microbial communities" by Stefanie Imminger, Dimitri Meier, Arno Schintlmeister, Anton Legin, Jörg Schnecker, Andreas Richter, Osnat Gillor, Stephanie A. Eichorst, and Dagmar Woebken.

Data availability: Metatranscriptomic reads have been deposited in the European Nucleotide Archive under project number PRJEB52014.

DISCLAIMER:

The authors consider themselves as microbial ecologists (not bioinformaticians) applying existing bioinformatic tools to analyze large amounts of RNA seqeuncing data. Scripts published here are meant to provide transparency about the parameters used in the analyses. They use only existing software and are not intended to constitute a ready-to-go pipeline. The scripts include parameters specific to the Vienna Life Sciences Computing cluster such as use of locally available databases and SLURM work-load manager etc.

The scripts in each folder are numbered. If two scripts have the same number, it means that these analyses do not depend on each other's output and can be run simultaneously.