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Detect chimeras by comparing sequences to a reference database

Source: R/vs_uchime_ref.R
vs_uchime_ref.Rd

vs_uchime_ref detects chimeras present in the FASTA sequences in using VSEARCH's uchime_ref algorithm.

Usage

vs_uchime_ref(
  fasta_input,
  database,
  nonchimeras = NULL,
  chimeras = NULL,
  sizein = TRUE,
  sizeout = TRUE,
  relabel = NULL,
  relabel_sha1 = FALSE,
  fasta_width = 0,
  sample = NULL,
  log_file = NULL,
  threads = 1,
  vsearch_options = NULL,
  tmpdir = NULL
)

Arguments

fasta_input

(Required). A FASTA file path or a FASTA object with reads. See Details.

database

(Required). A FASTA file path or FASTA tibble object containing the reference sequences. These sequences are assumed to be chimera-free.

nonchimeras

(Optional). Name of the FASTA output file for the non-chimeric sequences. If NULL (default), no output is written to file.

chimeras

(Optional). Name of the FASTA output file for the chimeric sequences. If NULL (default), no output is written to file.

sizein

(Optional). If TRUE (default), abundance annotations present in sequence headers are taken into account.

sizeout

(Optional). If TRUE (default), abundance annotations are added to FASTA headers.

relabel

(Optional). Relabel sequences using the given prefix and a ticker to construct new headers. Defaults to NULL.

relabel_sha1

(Optional). If TRUE (default), relabel sequences using the SHA1 message digest algorithm. Defaults to FALSE.

fasta_width

(Optional). Number of characters per line in the output FASTA file. Defaults to 0, which eliminates wrapping.

sample

(Optional). Add the given sample identifier string to sequence headers. For instance, if the given string is "ABC", the text ";sample=ABC" will be added to the header. If NULL (default), no identifier is added.

log_file

(Optional). Name of the log file to capture messages from VSEARCH. If NULL (default), no log file is created.

threads

(Optional). Number of computational threads to be used by VSEARCH. Defaults to 1.

vsearch_options

(Optional). Additional arguments to pass to VSEARCH. Defaults to NULL. See Details.

tmpdir

(Optional). Path to the directory where temporary files should be written when tables are used as input or output. Defaults to NULL, which resolves to the session-specific temporary directory (tempdir()).

Value

A tibble or NULL.

If nonchimeras and chimeras are specified, the resulting sequences after chimera detection written directly to the specified files in FASTA format, and no tibbles are returned.

If nonchimeras and chimeras are NULL, A FASTA object containing non-chimeric sequences with an attribute "chimeras" containing a tibble of chimeric sequences is returned. If no chimeras are found, the "chimeras" attribute is an empty data frame.

Additionally, the returned tibble (when applicable) has an attribute "statistics" containing a tibble with chimera detection statistics.

The statistics tibble has the following columns:

  • num_nucleotides: Total number of nucleotides used as input for chimera detection.

  • num_sequences: Total number of sequences used as input for chimera detection.

  • min_length_input_seq: Length of the shortest sequence used as input for chimera detection.

  • max_length_input_seq: Length of the longest sequence used as input for chimera detection.

  • avg_length_input_seq: Average length of the sequences used as input for chimera detection.

  • num_non_chimeras: Number of non-chimeric sequences.

  • num_chimeras: Number of chimeric sequences.

  • input: Name of the input file/object for the chimera detection.

Details

Chimeras in the input FASTA sequences are detected using VSEARCH´s uchime_ref.

fasta_input can either be a FASTA file or a FASTA object. FASTA objects are tibbles that contain the columns Header and Sequence, see readFasta.

database must be a FASTA file or a FASTA object with high-quality non-chimeric sequences.

vsearch_options allows users to pass additional command-line arguments to VSEARCH that are not directly supported by this function. Refer to the VSEARCH manual for more details.

References

https://github.com/torognes/vsearch

https://github.com/torognes/vsearch

Examples

if (FALSE) { # \dontrun{
# Define arguments
query_file <- file.path(file.path(path.package("Rsearch"), "extdata"),
                        "small.fasta")
db <- file.path(file.path(path.package("Rsearch"), "extdata"),
                "sintax_db.fasta")

# Detect chimeras with default parameters and return FASTA files
vs_uchime_ref(fasta_input = query_file,
              database = db,
              nonchimeras = "nonchimeras.fa",
              chimeras = "chimeras.fa")

# Detect chimeras with default parameters and return a FASTA tibble
nonchimeras.tbl <- vs_uchime_ref(fasta_input = query_file,
                                 database = db,
                                 nonchimeras = NULL,
                                 chimeras = NULL)

# Get chimeras tibble
chimeras.tbl <- attr(nonchimeras.tbl, "chimeras")

# Get statistics tibble
statistics.tbl <- attr(nonchimeras.tbl, "statistics")
} # }