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Detect for chimera taxa using vsearch

Source: R/vsearch.R
chimera_detection_vs.Rd

lifecycle-experimental

Use the VSEARCH software.

Usage

chimera_detection_vs(
  seq2search,
  nb_seq,
  vsearchpath = "vsearch",
  abskew = 2,
  min_seq_length = 100,
  vsearch_args = "--fasta_width 0",
  keep_temporary_files = FALSE
)

Arguments

(required) a list of DNA sequences coercible by function Biostrings::DNAStringSet()

nb_seq

(required) a numeric vector giving the number of sequences for each DNA sequences

vsearchpath

(default: vsearch) path to vsearch

abskew

(int, default 2) The abundance skew is used to distinguish in a three way alignment which sequence is the chimera and which are the parents. The assumption is that chimeras appear later in the PCR amplification process and are therefore less abundant than their parents. The default value is 2.0, which means that the parents should be at least 2 times more abundant than their chimera. Any positive value equal or greater than 1.0 can be used.

min_seq_length

(int, default 100)) Minimum length of sequences to be part of the analysis

vsearch_args

(default "–fasta_width 0") A list of other args for vsearch command

keep_temporary_files

(logical, default: FALSE) Do we keep temporary files ?

  • non_chimeras.fasta

  • chimeras.fasta

  • borderline.fasta

Value

A list of 3 including non-chimera taxa ($non_chimera), chimera taxa ($chimera) and bordeline taxa ($borderline)

Details

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

See also

chimera_removal_vs(), dada2::removeBimeraDenovo()

Author

Adrien Taudière

Examples

# \donttest{
chimera_detection_vs(
  seq2search = data_fungi@refseq,
  nb_seq = taxa_sums(data_fungi)
)
#> Filtering for sequences under 100 bp remove a total of 0 ( 0 %) unique sequences for a total of 0 sequences removed ( 0 %)
#> $non_chimera
#> AAStringSet object of length 1088:
#>        width seq                                            names               
#>    [1]   312 AAATGCGATAAGTAATGTGAAT...TAGGAATACCCGCTGAACTTA Taxa1;size=92884
#>    [2]   301 AAATGCGATAAGTAATGTGAAT...TAGGAATACCCGCTGAACTTA Taxa2;size=53538
#>    [3]   349 AAATGCGATAAGTAATGTGAAT...TGGGACTACCCGCTGAACTTA Taxa3;size=47410
#>    [4]   357 AAATGCGATAAGTAATGTGAAT...TGGGACTACCCGCTGAACTTA Taxa4;size=46857
#>    [5]   300 AAATGCGATAAGTAATGTGAAT...TAGGAATACCCGCTGAACTTA Taxa5;size=41082
#>    ...   ... ...
#> [1084]   260 AAACGCGAAAAGTGTTATGATG...AAGATCACCCGCTGAACTTAA Taxa1420;size=2
#> [1085]   365 AAATGCGATAAGTAATGTGAAT...TAGGACTACCCGCTGAACTTA Taxa602;size=2
#> [1086]   344 AAATGCGATAAGTAATGTGAAT...TAGGAATACGCGCTGAACTTA Taxa1142;size=1
#> [1087]   290 GAAATGCGATAAGTAATGTGAA...TAGGGATACCCGCTGAACTTA Taxa246;size=1
#> [1088]   318 GAAATGCGATACGTAATGTGAA...AGGGATACCCGCTGAACTTAA Taxa412;size=1
#> 
#> $chimera
#> AAStringSet object of length 220:
#>       width seq                                             names               
#>   [1]   341 GAAATGCGATAAGTAATGTGAA...GTAGGATTACCCGCTGAACTTA Taxa136;size=2743
#>   [2]   307 AAATGCGATAAGTAATGTGAAT...GTAGGGATACCCGCTGAACTTA Taxa163;size=2028
#>   [3]   339 AAATGCGATAAGTAATGTGAAT...GTAGGATTACCCGCTGAACTTA Taxa206;size=1471
#>   [4]   312 AAATGCGATAAGTAATGTGAAT...GTAGGAATACCCGCTGAACTTA Taxa286;size=875
#>   [5]   306 AAATGCGAAAAGTAGTGTGAAT...GTAGGGATACCCGCTGAACTTA Taxa294;size=832
#>   ...   ... ...
#> [216]   296 AAATGCGATACTTGGTGTGAAT...GTAGGGATACCCGCTGAACTTA Taxa1386;size=30
#> [217]   287 AAATGCGATAAGTAATATGAAT...GTAGGGATACCCGCTGAACTTA Taxa1389;size=29
#> [218]   293 GAACTACGATAAGTAATGTGAA...TAGGGATACCCGCTGAACTTAA Taxa1395;size=25
#> [219]   382 AAATGCGATAAATAATATGAAT...GCAAGATTACCCGCTGAACTTA Taxa1411;size=12
#> [220]   287 GAAATGCGATAAGTAATGTGAA...TAGGGCTACCCGCTGAACTTAA Taxa789;size=2
#> 
#> $borderline
#> AAStringSet object of length 112:
#>       width seq                                             names               
#>   [1]   298 AAATGCGATAAGTAATGTGAAT...GTAGGGATACCCGCTGAACTTA Taxa123;size=3164
#>   [2]   300 AAATGCGATAAGTAATGTGAAT...GTAGGGATACCCGCTGAACTTA Taxa139;size=2712
#>   [3]   295 AAATGCGATAAGTAATGTGAAT...GTAGGGATACCCGCTGAACTTA Taxa153;size=2294
#>   [4]   302 AAATGCGATAAGTAATGTGAAT...GTAGGGATACCCGCTGAACTTA Taxa174;size=1851
#>   [5]   383 AAATGCGATAAGTAATGTGAAT...GTGGGACTACCCGCTGAACTTA Taxa177;size=1814
#>   ...   ... ...
#> [108]   332 AAATGCGATAAGTAATGTGAAT...GTAGGAATACCCGCTGAACTTA Taxa1353;size=48
#> [109]   313 AAATGCGATAAGTAGTGTGAAT...TAGGAATACCCGCTGAACTTAA Taxa1354;size=48
#> [110]   300 GAAATGCGATAAGTAATGCGAA...GTAGGGATACCCGCTGAACTTA Taxa1384;size=31
#> [111]   302 GAAATGCGATACGTAATGTGAA...TAGGAATACCCGCTGAACTTAA Taxa1388;size=29
#> [112]   316 GAAATGCGATAAATAATATGAA...ACAAGATTACCCGCTGAACTTA Taxa1399;size=22
#> 
# }