dada2: derepFastq – R documentation

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derepFastq

Read in and dereplicate a fastq file.

Description

A custom interface to FastqStreamer for dereplicating amplicon sequences from fastq or compressed fastq files, while also controlling peak memory requirement to support large files.

Usage

derepFastq(fls, n = 1e+06, verbose = FALSE, qualityType = "Auto")

Arguments

`fls`	(Required). `character`. The file path(s) to the fastq file(s), or a directory containing fastq file(s). Compressed file formats such as .fastq.gz and .fastq.bz2 are supported.
`n`	(Optional). `numeric(1)`. The maximum number of records (reads) to parse and dereplicate at any one time. This controls the peak memory requirement so that large fastq files are supported. Default is `1e6`, one-million reads. See `FastqStreamer` for details on this parameter, which is passed on.
`verbose`	(Optional). Default FALSE. If TRUE, throw standard R `message`s on the intermittent and final status of the dereplication.
`qualityType`	(Optional). `character(1)`. The quality encoding of the fastq file(s). "Auto" (the default) means to attempt to auto-detect the encoding. This may fail for PacBio files with uniformly high quality scores, in which case use "FastqQuality". This parameter is passed on to `readFastq`; see information there for details.

Value

A derep-class object or list of such objects.

Examples

# Test that chunk-size, `n`, does not affect the result.
testFastq = system.file("extdata", "sam1F.fastq.gz", package="dada2")
derep1 = derepFastq(testFastq, verbose = TRUE)
derep1.35 = derepFastq(testFastq, n = 35, verbose = TRUE)
all.equal(getUniques(derep1), getUniques(derep1.35)[names(getUniques(derep1))])

dada2

Accurate, high-resolution sample inference from amplicon sequencing data

v1.18.0

LGPL-3

Authors

Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes

Initial release

2020-08-07