Résumé
Supporting material for the publication :
Effect of changing swarm’s fastidious boundary value on environmental DNA clustering results (working title)
by Milena Königshofen and Frédéric Mahé
In this study, Königshofen & Mahé use three published metabarcoding SSU rRNA datasets (18S V4, 18S V9 and 16S V3V4 fasta files) to demonstrate the effect of swarm's fastidious option (https://github.com/torognes/swarm).
Fasta files are derived from publicly available raw fastq files, following the pre-clustering pipeline available athttps://github.com/frederic-mahe/fred-metabarcoding-pipeline
The three original publications are:- de Vargas et al. (2015): V9 eukaryotic data from the sunlit surface layer of the world’s open oceans (doi: 10.1126/science.1261605; bioproject: PRJEB6610),- Mahé et al. (2017): V4 eukaryotic data from surface soils of three lowland Neotropical rainforests (doi: 10.1038/s41559-017-0091; bioproject: PRJNA317860),- Alonso et al. (2020): V3V4 bacterial data from plants stems collected in Chinese rice terraces (doi: 10.1111/1462-2920.15114; bioproject: PRJNA573048).