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change amplicon argument to "cutadapt". set to TRUE and inform sequence primers to trim primers with cutadapt. add cutadapt step in singleend SOP (illumina/torrent).
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add extension argument to inform R1 R2 pattern for paired data
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fixes
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update wiki and usecase
https://forgemia.inra.fr/umrf/ranomaly/-/wikis/home#dada2-usage-according-to-raw-data-type