add

Generate plots

perl FastQFS_V1.0.pl -plotting Yes -fw <forward reads="" file=""> -rw <reverse reads="" file=""> -prefix <prefix for="" the="" output="" files=""> -sc <scoring system="" used="" (33="" or="" 64)=""> -gsize <expected genome="" size="" in="" mbs=""> -l <read length=""> </read></expected></scoring></prefix></reverse></forward>

Perform read filtering

perl FastQFS_V1.0.pl -filtering Yes -fw <forward reads="" file=""> -rw <reverse reads="" file=""> -prefix <prefix for="" the="" output="" files=""> -sc <scoring system="" used="" (33="" or="" 64)=""> -mq <base_quality_cutoff> -q <average read="" quality="" threshold=""> -l <length threshold=""> -plotting <yes no=""> -gsize <expected genome="" size="" in="" mbs=""> </expected></yes></length></average></base_quality_cutoff></scoring></prefix></reverse></forward>

OPTIONS:

File related options

-fw : File having the forward reads.
-rw : File having the reverse reads.
-prefix : Prefix for the output files (forward file, reverse file, single file and other log files).

Filtering parameters related options

-sc : Scores used for reads quality (33 - Sanger Phred+33, 64 - Solexa Solexa+64) [Default: 33]
-mq : Minimum quality threshold for a base to filter [Default: 3]
-q : Average quality threshold filter [Default: 20]
-l : Length threshold filter [Default: 100]
-gsize : Expected genome size in MBs to calculate reads coverage depth.

General options

-plotting : Plot length distribution table (Yes or No).
-filtering : Perform the data filtering or not (Yes or No).
-h : Help message.

Author: Rahul Sharma and Marco Thines

Institute: Bik-F, Senckenberg.

Date: 12th, June, 2014

Version: V1.0

Description:

This script to helps user in making decisions on the data filtering parameters. It shows reads statistics

by calculating average quality, length and minimum quality of a base of both pairs. It considers average

qualities of 18 to 30 (increment of 4) and minimum base quality from 3 to 18 (increment of 5) and lengths

from L-50 (L is user-specified length) with the increment of 10. Later it can also filter out the reads

using following criteria:

1). Reads average quality cutoff.

2). Whole read will be discarded if one of the base is having quality below

the provided quality cutoff.

3). Reads which are shorter than the provided length cutoffs.

4). Reads which are having Ns.

Please cite using the following information:

Sharma R, Thines M: FastQFS – A tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing. Mycological Progress 2015, 14(8).