Search for a list of sequence in an object to remove chimera taxa using vsearch

Use the VSEARCH software.

Usage

chimera_removal_vs(object, type = "Discard_only_chim", clean_pq = FALSE, ...)

Arguments

object

(required) A phyloseq-class object or one of dada, derep, data.frame or list coercible to sequences table using the function dada2::makeSequenceTable()

type

(default "Discard_only_chim"). The type define the type of filtering.

"Discard_only_chim" will only discard taxa classify as chimera by vsearch
"Select_only_non_chim_seqlen_filtered" will only select taxa classify as non-chimera by vsearch(after filtering taxa based on their sequence length by the parameter min_seq_length from the chimera_detection_vs() function)
"Select_only_chim" will only select taxa classify as chimera by vsearch (after filtering taxa based on their sequence length by the parameter min_seq_length from the chimera_detection_vs() function)

clean_pq

(logical; default FALSE) If TRUE, return the phyloseq object after cleaning using the default parameter of clean_pq() function.

...

Additional arguments passed on to chimera_detection_vs() function

Value

I/ a sequences tables if object is of class dada, derep, data.frame or list.
II/ a phyloseq object without (or with if type = 'Select_only_chim') chimeric taxa

Details

This function is mainly a wrapper of the work of others. Please cite vsearch.

Author

Adrien Taudière

Examples

# \donttest{
# Adding a chimeric sequence for the example
data_fungi_with_chim <- data_fungi
data_fungi_with_chim@refseq["ASV1710"] <- Biostrings::xscat(
  Biostrings::subseq(data_fungi_with_chim@refseq[1], start = 1, end = 150),
  Biostrings::subseq(data_fungi_with_chim@refseq[4], start = 151, end = 300)
)
data_fungi_nochim <- chimera_removal_vs(data_fungi)
#> Filtering for sequences under 100 bp remove a total of 0 ( 0 %) unique sequences for a total of 0 sequences removed ( 0 %)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 240
#> Number of kept ASV 1180
#> Number of kept samples 185

# Higher value of abskew parameter is less stringent
data_fungi_nochim_16 <- chimera_removal_vs(data_fungi,
  abskew = 16,
  min_seq_length = 10
)
#> Filtering for sequences under 10 bp remove a total of 0 ( 0 %) unique sequences for a total of 0 sequences removed ( 0 %)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 159
#> Number of kept ASV 1261
#> Number of kept samples 185

# Potential Chimeric ASVs detected by vsearch
chim_asv <- taxa_names(data_fungi_with_chim)[!taxa_names(data_fungi_with_chim)
  %in% taxa_names(data_fungi_nochim)]

"ASV1710" %in% chim_asv
#> [1] FALSE

track_wkflow(list(data_fungi_with_chim, data_fungi_nochim))
#> Compute the number of sequences
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#> Compute the number of clusters
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#> Compute the number of samples
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#>   nb_sequences nb_clusters nb_samples
#> 1      1839124        1420        185
#> 2      1789481        1180        185

data_fungi_nochim2 <-
  chimera_removal_vs(data_fungi, type = "Select_only_non_chim_seqlen_filtered")
#> Filtering for sequences under 100 bp remove a total of 0 ( 0 %) unique sequences for a total of 0 sequences removed ( 0 %)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 366
#> Number of kept ASV 1054
#> Number of kept samples 185
data_fungi_chimera <-
  chimera_removal_vs(data_fungi, type = "Select_only_chim")
#> Filtering for sequences under 100 bp remove a total of 0 ( 0 %) unique sequences for a total of 0 sequences removed ( 0 %)
#> Cleaning suppress 0 taxa (  ) and 14 sample(s) ( BA16-036bis_S20_MERGED.fastq.gz / C21-NV1-M_S64_MERGED.fastq.gz / CB8-019-B_S69_MERGED.fastq.gz / DY5-004-M_S98_MERGED.fastq.gz / E9-009-B_S100_MERGED.fastq.gz / H10-018-M_S110_MERGED.fastq.gz / N22-001-B_S129_MERGED.fastq.gz / N23-002-M_S132_MERGED.fastq.gz / O21-007-H_S143_MERGED.fastq.gz / O21-007-M_S144_MERGED.fastq.gz / O24-003-H_S146_MERGED.fastq.gz / X24-009-H_S171_MERGED.fastq.gz / Y28-002-B_S178_MERGED.fastq.gz / Y29-007-H_S182_MERGED.fastq.gz ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 1180
#> Number of kept ASV 240
#> Number of kept samples 171
# }