datasets, whose sizes tend to defy most attempts at manual processing and examination. Conflict of interest . Bengtsson-Palme et al. 2015), such as Metaxa2, which relies on the comparison of It is made available under a CC-BY-NC 4.0 International license. Fig. 7. Comparison of the overall annotation accuracy of the three algorithms, Blast+, Metaxa2 and SINTAX for all single HVR (A) and HVR pairs (B). Although Blast+ presented a slightly better performance over SINTAX and Metaxa2, it was not statistically significant. The DeepARG webservice (beta) is a tool with fully automated data analysis pipeline for Antibiotic Resistance annotation of raw metagenomics samples using the deepARG algorithm and our developed database (deepARG-DB). You just need to upload your raw sequence reads (*.fastq.gz) and our service will take care of everything else. The Metaxa2 classifier is capable of extracting sequences belonging to a specific locus of interest from multi-locus or metagenomic data using Service Cropland Data Layer 2018), OpenLayers aerial imagery (Map data provided by Google; Sourcepole 2018), and manual ground-truthing. Landscape features were classified into three categories: crop Using this database with the Metaxa2 classifier, we performed a cross-validation analysis to characterize the relationship between the Metaxa2 reliability score, an estimate of classification confidence, and classification error probability. We used this analysis to select a reliability score threshold which minimized error. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products. Background underpinning the Metaxa2 classification procedures. Prior to extraction, we randomly selected a reference sequence, trimmed it to the exact 157 bp barcode amplicon of interest A mini-test revealed that performance statistical descriptors was almost identical, indicating that the differences observed between Parallel-meta and Metaxa2 are independent of the blast The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species- or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. Since we are going to use the plotting functionality of R, we need to login to Uppmax with X11 forwarding turned on. In the Unix/Linux terminal this is easily achieved by adding the -X (captal X) option. All programs but Metaxa2 are already installed, all you have to do is load the virtual environment for this workshop. Curate Data and Train Metaxa2 Download sequence data from NCBI Nucleotide. rbcL, trnL, ITS2 and chloroplast genome sequences downloaded on 07/05/2018; trnH sequences downloaded on 01/23/2019; An example of the long, manual way for trnL Format tax lineages, clean up artifacts, extract marker using HMM-based IterRazor tool and dereplicate 104region using the Metaxa2 extractor (Bengtsson-Palme et al. 2015). To increase the accuracy of 105this process, we split the original input sequences on the basis of length prior to running the 106database builder for amplicon extraction, creating four files with sequences of 250-500 bp, 501- 104region using