Within the Biodiversity Genomics Europe project, the "High Mountain Systems - Arthropods" case study was designed to evaluate how arthropod communities change along altitudinal gradients in seven selected mountain systems across different countries in Europe, establishing baseline sampling in mountain ranges to track biodiversity shifts associated with climate change. This SOP describes the sampling design and fieldwork methodology for retrieving arthropod bulk samples for metabarcoding analyses. ...

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.

16S rRNA amplicon sequencing analysis workflow using QIIME2.

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SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible eDNA analyses using Nextflow. SAMBA starts processing by verifying integrity of raw reads and metadata. Then all bioinformatics processing is done using commonly used procedure (QIIME 2 and DADA2) but adds new steps relying on dbOTU3 and microDecon to build high quality ASV count tables. Extended statistical analyses are also performed. Finally, SAMBA ...