Publications

Dueholm2020a: "Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)" DOI: 10.1101/672873

• Data availability
  • The raw sequencing data is available at the European Nucleotide Archive with BioProject ID: PRJEB26558.
  • RMarkdown files for reproducing the figures are available at GitHub: Dueholm2019a
  • AutoTax processed versions of the SILVA_132_SSURef_Nr99 database in SINTAX and Qiime format is available at figshare: (https://figshare.com/articles/SILVA_132_NR99_AutoTax/12366620)
  • AutoTax processed versions of the SILVA_138_SSURef_Nr99 database in SINTAX and Qiime format is available at figshare: (https://figshare.com/articles/SILVA_138_NR99_AutoTax/12366626)
  • AutoTax processed versions of the FL-ASV and FL-OTU expanded databases used in the article in SINTAX and Qiime format is available at figshare: (https://figshare.com/articles/Data_used_in_AutoTax_paper/12377741/1)

Dueholm2022a: "MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants" DOI: 10.1038/s41467-022-29438-7

• Data availability
  • The raw and assembled sequencing data is available at the NCBI SRA database with BioProject ID: PRJNA728873.
  • RMarkdown files for reproducing the figures are available at GitHub: Dueholm2022a
  • Raw data files for the RMarkdown scripts are available at figshare: (https://doi.org/10.6084/m9.figshare.16566408.v1)
  • The MiDAS 4 database in SINTAX and QIIME format is available at the MiDAS homepage: (https://midasfieldguide.org/guide/downloads)

Overgaard2022a: "AsCoM: An ecosystem-specific reference database for increased taxonomic resolution in soil microbial profiling"

• Data availability
  • The raw sequencing data is available at the European Nucleotide Archive with BioProject ID: PRJNA787301.
  • RMarkdown files including raw data for reproducing the figures are available at GitHub: Overgaard2022a
  • The AsCoM database v1.0 in SINTAX and QIIME format is available at GitHub: Overgaard2022a

Dueholm2022b: "Genetic potential for exopolysaccharide synthesis in activated sludge bacteria uncovered by genome-resolved metagenomics"

• Data availability
  • R-scripts for reproducing the figures are available at GitHub: Dueholm2022b
  • Raw data files for the R-scripts are available at figshare: (https://doi.org/10.6084/m9.figshare.21287112.v1)

Overgaard2024: "Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes"

• Data availability
  • The raw sequencing data is available at the European Nucleotide Archive with BioProject ID: PRJNA1019781.
  • RMarkdown files including raw data for reproducing the figures are available at GitHub: Overgaard2024
  • Scripts used for data processing are available at GitHub: Overgaard2024