do_taxonomy_step: Construct Sequence Table, Remove Chimeras, and Assign...

Description Usage Arguments Value References Examples

Description

Construct Sequence Table, Remove Chimeras, and Assign Taxonomy

Usage

1
do_taxonomy_step(mergers, chim_method = "consensus", ref_db)

Arguments

mergers

merged pairs of sequences

chim_method

string for method of chimera removal, either "consensus" (default) or "pooled"

Value

Returns list of

seqtab

sequence table

seqtab_nochim

sequence table without chimeras

taxa

assigned taxonomy from sequence variants

References

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

Examples

1
2
refdb <- "greengenes.fa.gz"
do_taxonomy_step(mergers, ref_db = refdb)

erictleung/dada2HPCPipe documentation built on May 10, 2019, 1:19 p.m.