An Introduction to FastqCleaner

Leandro Roser1*, Fernán Agüero1 and Daniel Sánchez1

1IIB-INTECH - UNSAM

*learoser@gmail.com

Abstract

FastqCleaner is an interactive application for both quality control and pre-processing of FASTQ files. The interface, based on a Bioconductor back-end, provides diagnostic information for the input and output data and a series of filtering and trimming operations in an interactive framework.

Package

FastqCleaner 1.25.0

1 Launching the application

The interactive application can be launched in R with the following command:

library('FastqCleaner')
launch_fqc()

As an alternative method, an RStudio addin (RStudio version 0.99.878 or higher required) installed with the package can be found in the Addins menu (Figure 1). This button allows the direct launch of the application with a single click.

Figure 1: addin of the app in RStudio (RStudio version >= 0.99.878 required)

 

2 Description of the application

The application contains three main panels, as described below.

2.1 First panel

The first panel includes two elements: a dashboard for selection of trimming and filtering operations, and a menu for selection of the input file/s (Fig. 2).

Figure 2: Panel 1, with each compontent indicated with a number. See explanation for each element below

 

2.1.1 Selecting operations

The “operations menu” (Fig. 2, elements 1 to 8) shows the available operations for file processing:

1. Remove by N(s): removes sequences with a number of Ns (non identified bases) above a selected threshold value

2. Remove low complexity sequences: remove sequences with a value of complexity above a threshold value

3. Remove adapters: removes adapters and partial adapters. Adapter sequences from both ends of single or paired read reads can be selected. Sequences can be reverse-complemented before processing. The program also allows to consider indels and/or anchored adapters.

4. Filter by average quality: computes the average quality of sequences and removes those with a value below a given threshold

5. Trim low quality 3’ tails: removes the 3’ tails of sequences that are below a given threshold

6. Trim 3’ or 5’ by a fixed number: removes a fixed number of bases from the 3’ and/or 5’ ends in the complete set of sequences

7. Filter sequences by length: removes all the sequences with a number of bases below a threshold value

8. Remove duplicated sequences: removes duplicated reads, conserving only one copy of each sequence present in the file

2.1.2 Loading files

The “file selection menu” (Fig. 2, elements 9 to 17) contains options to handle the input file (type of file, file selection), buttons to run, clear and reset the aplication, and the “advanced” submenu:

9. Single-end reads / paired-end reads: type of input files

10. “FILE” button: to select an input file

11. “RUN!” button: to run the program

12. Output format: to select whether the output file should be compressed (.gz) or not

13. “CLEAR” button: to clear the configuration of the operations menu that have been selected in the first panel, but keeping the input file(s)

14. “RESET” button: to restart the application, removing the input file(s) and the selected configurations

15. Selection notificator: information of the path of the selected file/s

16. Encoding notificator: information of the input file/s encoding

17. Advanced options button: to select a custom encoding and set the number of reads included in each chunk for processing, as described below

2.1.3 Advanced options

The “advanced options submenu” (Fig. 3) allows to customize some fine aspects of the trimming and filtering process: