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)

### Arguments

`fls` | (Required). `character`. The file path(s) to the fastq or fastq.gz file(s). Actually, any file format supported by `FastqStreamer`.
`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.

### 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, 35, TRUE)
    all.equal(getUniques(derep1), getUniques(derep1.35)[names(getUniques(derep1))])

[Package dada2 version 1.10.1 Index]