derepFastq {dada2} | R Documentation

## 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))])

[Package dada2 version 1.18.0 Index]