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 1.12.0 Index]