Description Usage Arguments Value References Examples
Construct Sequence Table, Remove Chimeras, and Assign Taxonomy
1 | do_taxonomy_step(mergers, chim_method = "consensus", ref_db)
|
mergers |
merged pairs of sequences |
chim_method |
string for method of chimera removal, either "consensus" (default) or "pooled" |
Returns list of
seqtab
sequence table
seqtab_nochim
sequence table without chimeras
taxa
assigned taxonomy from sequence variants
See "Construct sequence table" http://benjjneb.github.io/dada2/tutorial.html#construct-sequence-table
See "Remove chimeras" http://benjjneb.github.io/dada2/tutorial.html#remove-chimeras
See "Assign taxonomy" http://benjjneb.github.io/dada2/tutorial.html#assign-taxonomy
1 2 | refdb <- "greengenes.fa.gz"
do_taxonomy_step(mergers, ref_db = refdb)
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