Detect chimeric taxa with dada2 or vsearch

Flags chimeric taxa using either dada2::removeBimeraDenovo() de novo detection (method = "dada2") or UCHIME reference-based detection via vsearch (method = "vsearch_ref").

This is a pure detector: it flags taxa and returns a contam_tbl without modifying physeq. Use filter_contam_pq() to remove the flagged taxa.

Usage

identify_contam_chimera_pq(
  physeq,
  method = c("dada2", "vsearch_ref"),
  dada2_method = "consensus",
  database = NULL,
  vsearchpath = "vsearch",
  vsearch_args = "--fasta_width 0",
  keep_temporary_files = FALSE,
  verbose = TRUE,
  ...
)

Arguments

physeq

(phyloseq, required) A phyloseq object with a populated @refseq slot containing DNA sequences.

method

(character, default "dada2") Detection engine: "dada2" for de novo abundance-based detection, or "vsearch_ref" for reference-based UCHIME detection (requires database).

dada2_method

(character, default "consensus") Passed as method to dada2::removeBimeraDenovo() when method = "dada2". One of "consensus", "pooled", "per-sample".

database

(character, default NULL) Path to the reference FASTA database used by vsearch. Required when method = "vsearch_ref".

vsearchpath

(character, default "vsearch") Path to the vsearch executable.

vsearch_args

(character, default "--fasta_width 0") Extra arguments passed verbatim to vsearch.

keep_temporary_files

(logical, default FALSE) Keep the temporary FASTA files written to tempdir() (vsearch only).

verbose

(logical, default TRUE) Print a one-line detection summary.

...

Additional arguments passed to dada2::removeBimeraDenovo().

Value

A contam_tbl with one row per chimeric taxon, method = "chimera", and the evidence columns chimera_method ("dada2" or "vsearch_ref") and n_reads. Empty when no chimera is detected.

See also

filter_contam_pq() to remove flagged taxa, create_chimera_pq() to generate synthetic chimeras for benchmarking.

Author

Adrien Taudière

Examples

library(MiscMetabar)
data(data_fungi)
# \donttest{
flagged <- identify_contam_chimera_pq(data_fungi, method = "dada2")
#> ℹ chimera (dada2): flagged 450 of 1420 taxa.
flagged
#> contam_tbl: 450 flagged taxons from methods "chimera"
#> # A tibble: 450 × 4
#>    taxon  method  chimera_method n_reads
#>    <chr>  <chr>   <chr>            <dbl>
#>  1 ASV94  chimera dada2             5842
#>  2 ASV120 chimera dada2             4558
#>  3 ASV128 chimera dada2             4298
#>  4 ASV158 chimera dada2             3193
#>  5 ASV159 chimera dada2             3164
#>  6 ASV170 chimera dada2             2860
#>  7 ASV178 chimera dada2             2743
#>  8 ASV182 chimera dada2             2712
#>  9 ASV186 chimera dada2             2611
#> 10 ASV201 chimera dada2             2294
#> # ℹ 440 more rows
# }