unique_filter {FastqCleaner} | R Documentation

## Remove duplicated sequences in a FASTQ file

### Description

This program is a wrapper to `occurrenceFilter`. It removes the duplicated sequences of a FASTQ file.

### Usage

    unique_filter(input)

### Arguments

`input` | `ShortReadQ` object

### Value

Filtered `ShortReadQ` object

### Author(s)

Leandro Roser learoser@gmail.com

### Examples

    require('Biostrings')
    require('ShortRead')

    set.seed(10)
    s <- random_seq(10, 10)
    s <- sample(s, 30, replace = TRUE)
    q <- random_qual(30, 10)
    n <- seq_names(30)

    my_read <- ShortReadQ(sread = s, quality = q, id = n)

    # check presence of duplicates
    isUnique(as.character(sread(my_read)))

    # apply the filter
    filtered <- unique_filter(my_read)

    isUnique(as.character(sread(filtered)))

[Package FastqCleaner version 1.8.0 Index]