Rsearch (version 1.0.0)

vs_fastx_uniques: Dereplicate sequences

Description

vs_fastx_uniques performs dereplication of sequences in a FASTA/FASTQ file or object by merging identical sequences using VSEARCH.

Usage

vs_fastx_uniques(
  fastx_input,
  output_format = "fasta",
  fastx_output = NULL,
  minuniquesize = 1,
  strand = "plus",
  sizein = TRUE,
  sizeout = TRUE,
  relabel = NULL,
  relabel_sha1 = FALSE,
  fastq_qout_max = FALSE,
  fasta_width = 0,
  sample = NULL,
  vsearch_options = NULL,
  tmpdir = NULL
)

Value

A tibble or NULL.

If fastx_output is specified, the dereplicated sequences are written to the specified output file, and no tibble is returned.

If fastx_output

NULL, a tibble containing the dereplicated reads in the format specified by output_format is returned.

Arguments

fastx_input

(Required). A FASTA/FASTQ file path or FASTA/FASTQ object. See Details.

output_format

(Optional). Desired output format of file or tibble: "fasta" (default) or "fastq". If fastx_input is a FASTA file path or a FASTA object, output_format cannot be "fastq".

fastx_output

(Optional). Name of the output file for dereplicated reads from fastx_input. File can be in either FASTA or FASTQ format, depending on output_format. If NULL (default), no sequences are written to file. See Details.

minuniquesize

(Optional). Minimum abundance value post-dereplication for a sequence not to be discarded. Defaults to 1.

strand

(Optional). Specifies which strand to consider when comparing sequences. Can be either "plus" (default) or "both".

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.

fastq_qout_max

(Optional). If TRUE, the quality score will be the highest (best) quality score observed in each position. 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 nstance, if the given string is "ABC", the text ";sample=ABC" will be added to the header. If NULL (default), no identifier is added.

vsearch_options

(Optional). A character string of 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()).

Details

Sequences in the input file/object (fastx_input) are dereplicated by merging identical sequences. Identical sequences are defined as sequences with the same length and the same string of nucleotides (case insensitive, T and U are considered the same).

fastx_input can either be a FASTA/FASTQ file or a FASTA/FASTQ object. FASTA objects are tibbles that contain the columns Header and Sequence, see readFasta. FASTQ objects are tibbles that contain the columns Header, Sequence, and Quality, see readFastq.

By default, the quality scores in FASTQ output files will correspond to the average error probability of the nucleotides in the each position. If fastq_qout_max = TRUE, the quality score will be the highest (best) quality score observed in each position.

If fastx_output is specified, the dereplicated sequences are output to this file in format given by output_format. If fastx_output is NULL, the dereplicated sequences are returned as a FASTA or FASTQ object, depending on output_format.

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

Examples

if (FALSE) {
# Define arguments
fastx_input <- file.path(file.path(path.package("Rsearch"), "extdata"),
                         "small_R1.fq")
fastx_output <- NULL
output_format <- "fastq"

# Dereplicate sequences and return a FASTQ tibble
derep_R1 <- vs_fastx_uniques(fastx_input = fastx_input,
                             fastx_output = fastx_output,
                             output_format = output_format)

# Dereplicate sequences and write derelicated sequences to a file
vs_fastx_uniques(fastx_input = fastx_input,
                 fastx_output = "dereplicated_sequences.fq",
                 output_format = output_format)
}