Remove duplicated sequences in a FASTQ file — unique_filter • FastqCleaner
Description: This program is a wrapper to occurrenceFilter. It removes the duplicated sequences of a FASTQ file.

# Remove duplicated sequences in a FASTQ file

`unique_filter.Rd`

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

    unique_filter(input)

## Arguments

input | `ShortReadQ` object

## Value

Filtered `ShortReadQ` object

## 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)))#>  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE
    #> [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
    #> [25] FALSE FALSE FALSE FALSE FALSE FALSE
    # apply the filter
    filtered <- unique_filter(my_read)

    isUnique(as.character(sread(filtered)))#> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE