ParseTaxonomy: ParseTaxonomy

In leholman/metabarTOAD: A group of simple functions for handling metabarcoding data

ParseTaxonomy

Description

This function parses taxonomy from a BLAST query to provide assignments at a given identity. An example blast command to use to generate a dataset to use for assignbments might be blastn -query ../path/to/your/seqs.fasta -db nt -out ../path/to/your/resultsfolder/results.txt -outfmt '6 qseqid qlen slen qcovs qcovhsp sseqid bitscore score evalue pident qstart qend sstart send staxids sscinames' -num_alignments 25 -num_threads 1

Usage

ParseTaxonomy(
  pctThreshold = 97,
  covpct = 90,
  lwrpctThreshold = 85,
  lwrcovpct = 65,
  blastoutput = NA,
  lineages = NA,
  returntable = TRUE
)

Arguments

pctThreshold	Percent identity match threashold for high quality assignments, 97-100 depending on marker
covpct	Percent coverage of hit to be considered high quality
lwrpctThreshold	Percent identity match threshold under which a hit is not considered
lwrcovpct	Percent coverage of hit under which a hit is not considered
blastoutput	The full directory to a text file with output from the BLAST standalone executable
lineages	The full directory to a text file containing lineage information for each NCBI taxonomy number
returntable	Return a table showing the assignments by catagory?

Value

Returns a data frame object containing assignments

leholman/metabarTOAD documentation built on Aug. 27, 2023, 9:07 p.m.