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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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pruning taxa using sequence lengths (width) #1769

Closed sghignone closed 2 months ago

sghignone commented 2 months ago

Hi, given a phyloseq object which includes the refseq slot (DNAStringSet), is there any smart and not tricky way to get rid of ASV with sequences shorter than a give threshold? Any hint is welcome, cheers, SG

sghignone commented 2 months ago

ps <- prune_taxa(width(refseq(ps)) => 200, ps)