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Detect chimeras without external references (i.e. de novo)

Source: R/vs_uchime_denovo.R
vs_uchime_denovo.Rd

vs_uchime_denovo detects chimeras present in the FASTA sequences in using VSEARCH's uchime_denovo algorithm. Automatically sorts sequences by decreasing abundance to enhance chimera detection accuracy.

Usage

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

Arguments

fasta_input

(Required). A FASTA file path or a FASTA object with reads. If a tibble is provided, any columns in addition to Header and Sequence will be preserved in the output. See Details.

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.

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 is returned. This output tibble will include any additional columns that were present in the fasta_input tibble. An attribute named "chimeras" will contain a tibble of the chimeric sequences, also with the additional columns preserved.

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_denovo. In de novo mode, input FASTA file/object must present abundance annotations (i.e. a pattern [;]size=integer[;] in the header). Input order matters for chimera detection, so it is recommended to sort sequences by decreasing abundance.

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.

When providing a tibble as fasta_input, you can include additional columns with metadata (e.g., OTU IDs, sample origins). The function will preserve these columns by joining them back to the results based on the DNA sequence. This allows you to keep your metadata associated with your sequences throughout the chimera detection process.

If nonchimeras and chimeras are specified, resulting non-chimeric and chimeric sequences are written to these files in FASTA format.

If nonchimeras and chimeras are NULL, results are returned as a FASTA-objects.

nonchimeras and chimeras must either both be specified or both be NULL.

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
fasta_input <- file.path(file.path(path.package("Rsearch"), "extdata"),
                         "small_R1.fq")
nonchimeras <- "nonchimeras.fa"
chimeras <- "chimeras.fa"

# Detect chimeras with default parameters and return FASTA files
vs_uchime_denovo(fasta_input = fasta_input,
                 nonchimeras = nonchimeras,
                 chimeras = chimeras)

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

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

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