Fig. 1

Detection of sRNAs in Oasis 2: The web application allows for the upload of raw or compressed FASTQ files to Oasis 2’s sRNA detection module. After pre-processing (adapter/barcode trimming and length filtering), reads are first aligned to target organism (TO) transcripts that are stored in Oasis-DB (Step 1), including known miRNAs, piRNAs, snoRNAs, snRNAs, rRNAs, and high-stringency predicted miRNAs and their families. Unmapped reads of Step1 are subsequently aligned to the TO’s genome (Step 2) to predict and subsequently store novel miRNAs in Oasis-DB. Unmapped reads from step 2 are mapped to bacterial, archaeal, and viral genomes using Kraken (Step 3) to detect potential pathogenic infections or contaminations. Finally, reads that could not be aligned in steps 1–3 are aligned to all non-target organism (NTO) miRNAs in miRBase (Step 4) to detect potentially orthologous or cross-species miRNAs. In case the user’s data does not correspond to one of the 14 supplied organisms, Oasis 2 aligns the reads only to NTO miRNAs (Step 4), supporting the detection of miRNA expression in any organism