Complementary Material - Wegner et al., 2023 doi: https://doi.org/10.1186/s40168-023-01647-2 ------------------------------------------------- ***A glimpse of the paleome in endolithic microbial communities*** ------------------------------------------------------------------------ Carl-Eric Wegner¹, Raphaela Stahl², Irina Velsko², Alex Hübner², Zandra Fagernäs², Christina Warinner^2,3,6, Robert Lehmann⁴, Thomas Ritschel⁴, Kai U. Totsche^4,6, Kirsten Küsel^1,5,6 ¹ Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Dornburger Str. 159, 07743 Jena, Germany ² Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ³ Department of Anthropology, Harvard University, Cambridge, MA, USA ⁴ Institute of Geosciences, Hydrogeology, Friedrich Schiller University Jena, Burgweg 11, 07749 Jena, Germany ⁵ German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany ⁶ Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany Correspondence should be addressed to: [**Kirsten Küsel**][1] ------- This repository provides complementary material for the manuscript Wegner et al., 2023. We provide here essential intermediate files with respect to data processing, data analysis, and key findings. In addition, we describe important steps of data processing and analysis in form of detailed walkthroughs. If you visit this repository and run into any issue, do not hesitate to contact [**Carl-Eric Wegner**][2]. ------- We provide the following intermediate files/resources: * [_assembled contigs_](https://osf.io/v8gsd/files/osfstorage/6343c8da31d65315602dca27), assemblies were done as outlined here: [`Sequence data pre-processing, estimation of metagenome coverage, and metagenome assembly `](https://osf.io/v8gsd/wiki/pre_processing/) * [_`.bam` files from mapping QCed sequences onto assembled contigs_](https://osf.io/v8gsd/files/osfstorage/6343ca8ed5b0101fda1f7cee), the steps involved in generating the mapping files are described here: [`Sequence data pre-processing, estimation of metagenome coverage, and metagenome assembly `](https://osf.io/v8gsd/wiki/pre_processing/) * [_DNA damage profiles (per assembly/data set)_](https://osf.io/v8gsd/files/osfstorage/6343cb1bec7f3f2052f5f64e), information about DNA damage pattern analysis can be accessed here: [`DNA damage pattern analysis`](https://osf.io/v8gsd/wiki/DNA_dmg_analyis/), the `.zip` file includes two tables, one including the damage profiles for all contigs per data set, and one only based on _Cand. Rokubacteria_ contigs * [_Cand. Rokubacteria contigs_](https://osf.io/v8gsd/files/osfstorage/6343cbeb24289c201fc12e65), these contigs were subsambled from the "total" assemblies per data set, the subsambpling was based on determining the taxonomic affiliations of contigs with _kaiju_ * [_`.bam` files from mapping QCed sequences onto _Cand. Rokubacteria_ contigs_](https://osf.io/v8gsd/files/osfstorage/6343ccdcec7f3f204af5fc2f), the mapping was done as described here: [`Sequence data pre-processing, estimation of metagenome coverage, and metagenome assembly `](https://osf.io/v8gsd/wiki/pre_processing/), **BUT** using the _Cand. Rokubacteria contigs_ mentioned above as reference, resulting `.bam` files were filtered and sequences <30 bp removed * [_a python script_](https://github.com/biobakery/humann), that we used to summarize the gene families table from _humann_, which was regrouped to KEGG orthologies and normalized to copies per million (CoPM), with respect to pathways and functions of interest ------- Below you find walkthroughs that encompass crucial processing and analysis steps with respect to this study: * [_Sequence data pre-processing, estimation of metagenome coverage, and metagenome assembly_](https://osf.io/v8gsd/wiki/pre_processing/) * [_Taxonomic and functional profiling_](https://osf.io/v8gsd/wiki/tax_func_profiling/) * [_DNA damage pattern analysis_](https://osf.io/v8gsd/wiki/DNA_dmg_analyis/) [1]: http://mailto:%20kirsten.kuesel@uni-jena.de [2]: http://mailto:%20carl-eric.wegner@uni-jena.de