map_seqvar: Assign seq vars to OTUs or AGORA models using vsearch

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Assign seq vars to OTUs or AGORA models using vsearch

Description

Assign seq vars to OTUs or AGORA models using vsearch

Usage

map_seqvar(
  seqs,
  repSeqDir = "data/AGORA/",
  repSeqFile = "agora_NCBI_16S.udb",
  method = "vsearch",
  vsearch_path = "vsearch",
  file_prefix = "seqtemp",
  seqID = 0.99,
  add_agora_names = T,
  add_embl_names = F,
  otu_tab = F
)

Arguments

seqs	vector of sequence variants
repSeqDir	File path to reference database
repSeqFile	File name with reference sequences
method	Only "vsearch" currently implemented
vsearch_path	Path to vsearch executable
file_prefix	File name prefix for output
seqID	threshold for vsearch –usearch-global search
add_agora_names	Whether to add AGORA IDs to the table
add_embl_names	Whether to add RefSeq/embl_gems names to the table
otu_tab	Whether to return an OTU table, or just the matched sequences

Value

Table of alignment results (original sequence, hit ID)

Examples

map_seqvar(seqs)

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.