Decona: From demultiplexing to consensus for Nanopore amplicon data

Sequencing of long amplicons is one the major benefits Nanopore technologies, as it allows for reads much longer than Illumina. One challenges analysis these relatively high error rate. errors are generally corrected by consensus generation and polishing. This still a challenge mixed samples such metabarcoding environmental DNA, bulk amplicon PCR’s contaminated because sequence data would have to be clustered before generation. To this end, we developed Decona (https://github.com/Saskia-Oosterbroek/decona), command line tool that creates sequences from (metabarcoding) using single command. uses CD-hit algorithm cluster after demultiplexing (qcat) filtering (NanoFilt). The in each subsequently aligned (Minimap2), generated (Racon) finally polished (Medaka). Variant calling clusters (Medaka) optional. With integration BLAST+ application does not only generate but also produces BLAST output if desired. program can used on laptop computer making suitable use under field conditions. Amplicon ranging 300-7500 nucleotides was successfully processed Decona, creating reaching over 99,9% read identity. included fish datasets (environmental DNA filtered water) curated aquarium, vertebrate were with human separating sponge their countless microbial symbionts. considerably simplifies speeds up post sequencing processes, providing through Classifying instead raw improves classification accuracy drastically decreases amount need classified. Overall user friendly option researchers limited knowledge script based processing.