fastqPairedFilter: Filters and trims paired forward and reverse fastq files.

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

Filters and trims paired forward and reverse fastq files.

Description

fastqPairedFilter filters pairs of input fastq files (can be compressed) based on several user-definable criteria, and outputs those read pairs which pass the filter in both directions to two new fastq file (also can be compressed). Several functions in the ShortRead package are leveraged to do this filtering. The filtered forward/reverse reads remain identically ordered.

Usage

fastqPairedFilter(
  fn,
  fout,
  maxN = c(0, 0),
  truncQ = c(2, 2),
  truncLen = c(0, 0),
  maxLen = c(Inf, Inf),
  minLen = c(20, 20),
  trimLeft = c(0, 0),
  trimRight = c(0, 0),
  minQ = c(0, 0),
  maxEE = c(Inf, Inf),
  rm.phix = c(TRUE, TRUE),
  rm.lowcomplex = c(0, 0),
  matchIDs = FALSE,
  orient.fwd = NULL,
  id.sep = "\\s",
  id.field = NULL,
  n = 1e+06,
  OMP = TRUE,
  qualityType = "Auto",
  compress = TRUE,
  verbose = FALSE,
  ...
)

Arguments

fn	(Required). A character(2) naming the paths to the (forward,reverse) fastq files.
fout	(Required). A character(2) naming the paths to the (forward,reverse) output files. Note that by default (compress=TRUE) the output fastq files are gzipped. FILTERING AND TRIMMING ARGUMENTS If a length 1 vector is provided, the same parameter value is used for the forward and reverse reads. If a length 2 vector is provided, the first value is used for the forward reads, and the second for the reverse reads.
maxN	(Optional). Default 0. After truncation, sequences with more than maxN Ns will be discarded. Note that dada currently does not allow Ns.
truncQ	(Optional). Default 2. Truncate reads at the first instance of a quality score less than or equal to truncQ.
truncLen	(Optional). Default 0 (no truncation). Truncate reads after truncLen bases. Reads shorter than this are discarded.
maxLen	(Optional). Default Inf (no maximum). Remove reads with length greater than maxLen. maxLen is enforced on the raw reads.
minLen	(Optional). Default 20. Remove reads with length less than minLen. minLen is enforced after all other trimming and truncation.
trimLeft	(Optional). Default 0. The number of nucleotides to remove from the start of each read. If both truncLen and trimLeft are provided, filtered reads will have length truncLen-trimLeft.
trimRight	(Optional). Default 0. The number of nucleotides to remove from the end of each read. If both truncLen and trimRight are provided, truncation will be performed after trimRight is enforced.
minQ	(Optional). Default 0. After truncation, reads contain a quality score below minQ will be discarded.
maxEE	(Optional). Default Inf (no EE filtering). After truncation, reads with higher than maxEE "expected errors" will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q/10))
rm.phix	(Optional). Default TRUE. If TRUE, discard reads that match against the phiX genome, as determined by isPhiX.
rm.lowcomplex	(Optional). Default 0. If greater than 0, reads with an effective number of kmers less than this value will be removed. The effective number of kmers is determined by seqComplexity using a Shannon information approximation. The default kmer-size is 2, and therefore perfectly random sequences will approach an effective kmer number of 16 = 4 (nucleotides) ^ 2 (kmer size).
matchIDs	(Optional). Default FALSE. Whether to enforce matching between the id-line sequence identifiers of the forward and reverse fastq files. If TRUE, only paired reads that share id fields (see below) are output. If FALSE, no read ID checking is done. Note: matchIDs=FALSE essentially assumes matching order between forward and reverse reads. If that matched order is not present future processing steps may break (in particular mergePairs).
orient.fwd	(Optional). Default NULL. A character string present at the start of valid reads. Only allows unambiguous nucleotides. This string is compared to the start of the forward and reverse reads. If it exactly matches the start of the forward read, the read is kept. If it exactly matches the start of the reverse read, the fwd/rev reads are swapped. Otherwise the read if filtered out. The primary use of this parameter is to unify the orientation of amplicon sequencing libraries that are a mixture of forward and reverse orientations, and that include the forward primer on the reads. ID MATCHING ARGUMENTS The following optional arguments enforce matching between the sequence identification strings in the forward and reverse reads, and can automatically detect and match ID fields in Illumina format, e.g: EAS139:136:FC706VJ:2:2104:15343:197393. ID matching is not required when using standard Illumina output fastq files.
id.sep	(Optional). Default "\s" (white-space). The separator between fields in the id-line of the input fastq files. Passed to the strsplit.
id.field	(Optional). Default NULL (automatic detection). The field of the id-line containing the sequence identifier. If NULL (the default) and matchIDs is TRUE, the function attempts to automatically detect the sequence identifier field under the assumption of Illumina formatted output.
n	(Optional). The number of records (reads) to read in and filter at any one time. This controls the peak memory requirement so that very large fastq files are supported. Default is 1e6, one-million reads. See FastqStreamer for details.
OMP	(Optional). Default TRUE. Whether or not to use OMP multithreading when calling FastqStreamer. Set this to FALSE if calling this function within a parallelized chunk of code (eg. within mclapply).
qualityType	(Optional). character(1). The quality encoding of the fastq file(s). "Auto" (the default) means to attempt to auto-detect the encoding. This parameter is passed on to readFastq; see information there for details.
compress	(Optional). Default TRUE. Whether the output fastq files should be gzip compressed.
verbose	(Optional). Default FALSE. Whether to output status messages.
...	(Optional). Arguments passed on to isPhiX or seqComplexity.

Value

integer(2). The number of reads read in, and the number of reads that passed the filter and were output.

See Also

fastqFilter FastqStreamer trimTails

Examples

testFastqF = system.file("extdata", "sam1F.fastq.gz", package="dada2")
testFastqR = system.file("extdata", "sam1R.fastq.gz", package="dada2")
filtFastqF <- tempfile(fileext=".fastq.gz")
filtFastqR <- tempfile(fileext=".fastq.gz")
fastqPairedFilter(c(testFastqF, testFastqR), c(filtFastqF, filtFastqR), maxN=0, maxEE=2)
fastqPairedFilter(c(testFastqF, testFastqR), c(filtFastqF, filtFastqR), trimLeft=c(10, 20),
                    truncLen=c(240, 200), maxEE=2, rm.phix=TRUE, rm.lowcomplex=5, kmerSize=2)

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.