unique_filter: Remove duplicated sequences in a FASTQ file

In FastqCleaner: A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files

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 [e-mail]

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)))

FastqCleaner documentation built on Nov. 8, 2020, 5:05 p.m.