truncate_and_merge_pairs: Truncate and Merge Forward and Reverse DNA Sequence Reads

In LocaTT: Geographically-Conscious Taxonomic Assignment for Metabarcoding

Truncate and Merge Forward and Reverse DNA Sequence Reads

Description

Removes DNA read pairs containing ambiguous nucleotides, truncates reads by length and quality score, and merges forward and reverse reads.

Usage

truncate_and_merge_pairs(
  forward_files,
  reverse_files,
  output_files,
  truncation_length = NA,
  threshold.quality_score = 3,
  threshold.probability = 0.5,
  minimum_overlap = 10,
  cores = 1,
  progress = FALSE
)

Arguments

forward_files	A character vector of file paths to FASTQ files containing forward DNA sequence reads.
reverse_files	A character vector of file paths to FASTQ files containing reverse DNA sequence reads.
output_files	A character vector of file paths to output FASTA files.
truncation_length	Numeric. The length to truncate DNA sequences to (passed to the length argument of truncate_sequences.length). If NA (the default), then DNA sequences are not truncated by length. If a single value is supplied, then both forward and reverse reads are truncated to the same length. If two values are supplied in a numeric vector, then the first value is used to truncate the forward reads, and the second value is used to truncate the reverse reads. NA can also be supplied as either the first or second element of the numeric vector to prevent length truncation of the respective read direction while allowing the other read direction to be length truncated.
threshold.quality_score	Numeric. The Phred quality score threshold used for truncation (passed to the threshold argument of truncate_sequences.quality_score). The default is 3 (i.e., each base in a truncated sequence has a greater than 50% probability of having been called correctly). If NA, then DNA sequences are not truncated by quality score threshold. If a single value is supplied, then both forward and reverse reads are truncated by the same quality score threshold. If two values are supplied in a numeric vector, then the first value is used to truncate the forward reads, and the second value is used to truncate the reverse reads. NA can also be supplied as either the first or second element of the numeric vector to prevent quality-score-threshold truncation of the respective read direction while allowing the other read direction to be quality-score-threshold truncated.
threshold.probability	Numeric. The probability threshold used for truncation (passed to the threshold argument of truncate_sequences.probability). The default is 0.5 (i.e., each truncated sequence has a greater than 50% probability that all bases were called correctly). If NA, then DNA sequences are not truncated by probability threshold. If a single value is supplied, then both forward and reverse reads are truncated by the same probability threshold. If two values are supplied in a numeric vector, then the first value is used to truncate the forward reads, and the second value is used to truncate the reverse reads. NA can also be supplied as either the first or second element of the numeric vector to prevent probability-threshold truncation of the respective read direction while allowing the other read direction to be probability-threshold truncated.
minimum_overlap	Numeric. The minimum length of an overlap that must be found between the end of the forward read and the start of the reverse complement of the reverse read in order for a read pair to be merged (passed to merge_pairs). The default is 10.
cores	Numeric. If 1 (the default), then FASTQ file pairs are processed sequentially on a single core. If greater than 1, then FASTQ file pairs are processed in parallel across the specified number of cores. Parallel processing is not supported on Windows.
progress	Logical. If TRUE, then a progress indicator is printed to the console. Ignored if cores > 1. If FALSE (the default), then no progress indicator is displayed.

Details

For each pair of input FASTQ files, removes DNA read pairs containing ambiguous nucleotides, truncates reads by length, quality score threshold, and probability threshold (in that order), and then merges forward and reverse reads. Merged reads are summarized by frequency of occurrence and written to a FASTA file. See contains_wildcards, truncate_sequences.length, truncate_sequences.quality_score, truncate_sequences.probability, and merge_pairs for methods. Quality scores are assumed to be encoded in Sanger format. Forward and reverse reads can be truncated by different thresholds (see truncation_length, threshold.quality_score, and threshold.probability arguments).

Multicore parallel processing is supported on Mac and Linux operating systems (not available on Windows). When cores > 1 (parallel processing enabled), warnings and errors are printed to the console in addition to being invisibly returned as a list (see the return value section), and errors produced while processing a pair of FASTQ files will not interrupt the processing of other FASTQ file pairs. When cores = 1, FASTQ file pairs are processed sequentially on a single core, and errors will prevent the processing of subsequent FASTQ file pairs (but warnings will not).

Value

If cores = 1, then no return value. Writes a FASTA file for each pair of input FASTQ files with DNA sequence counts stored in the header lines. If cores > 1, then also invisibly returns a list where each element contains warning or error messages associated with processing each pair of input FASTQ files. A NULL value in the returned list means that no warnings or errors were generated from processing the respective pair of FASTQ files.

References

A manuscript describing these methods is in preparation.

See Also

contains_wildcards for detecting ambiguous nucleotides in DNA sequences.

truncate_sequences.length for truncating DNA sequences to a specified length.

truncate_sequences.quality_score for truncating DNA sequences by Phred quality score.

truncate_sequences.probability for truncating DNA sequences by cumulative probability that all bases were called correctly.

merge_pairs for merging forward and reverse DNA sequence reads.

filter_sequences for filtering merged read pairs by PCR replicate.

Examples

# Get example forward FASTQ files.
forward_files<-system.file("extdata",
                           paste0("S0",1:3,"F.fastq"),
                           package="LocaTT",
                           mustWork=TRUE)

# Get example reverse FASTQ files.
reverse_files<-system.file("extdata",
                           paste0("S0",1:3,"R.fastq"),
                           package="LocaTT",
                           mustWork=TRUE)

# Create paths for temporary output files.
output_files<-tempfile(pattern=paste0("O",1:3),fileext=".fasta")

# Truncate and merge pairs.
truncate_and_merge_pairs(forward_files=forward_files,
                         reverse_files=reverse_files,
                         output_files=output_files)

LocaTT documentation built on June 14, 2026, 1:06 a.m.