dohalloran / fastQ_brew

filter fastQ file data

fastQ_brew v.2.0

• Pre-processing of FASTQ reads
• Check that files were demultiplexed correctly
• Filter reads by length
• Filter reads by quality
• Trim reads
• Removes standard Truseq adapters
• Performs various file conversions

Installation

1. Download and extract the fastQ_brew.zip file
   tar -xzvf fastQ_brew.zip or git clone https://github.com/dohalloran/fastQ_brew.git
2. The extracted dir will be called fastQ_brew

cd fastQ_brew   
perl Makefile.PL  
make  
make test  
make install  

Usage

To run:

use fastQ_brew;
use Moose;
use Modern::Perl;
use autodie;

my $app = fastQ_brew->new_with_options();
$app->run_fastQ_brew(); 
#see below for command flags

Command Line Arguments

Filtering Options

#set the max probability that a fastQ [1] read will contain errors: suggested p<=50% (must be 1-100)
       --qf 50
#filter by read length - reads below this length will be removed       
       --lf 35
#remove x bases from left end of every read 
       --trim_l 5
#remove x bases from right end of every read
       --trim_r 3
#remove standard truseq adapters (permits 1 mismatch) from both ends (very slow!)
       --truseq

File Conversions and de-multiplex check

#check that 2 FASTQ files were demultiplexed correctly 
#fastQ_brew outputs the barcodes for each file and compares (union and intersection) between two files 
       --plex
       -i <input_file1>
       -x <input_file2>
#convert FASTQ file to FASTA format file
       --fasta
#convert the DNA for each read to RNA 
       --dna_rna
#reverse complement the FASTQ reads 
       --rev_comp

Odds and Ends

#input FASTQ file (required) 
       --i <input_file>
#output FASTQ file (by default called filtered.fq) 
       --o <output_file>
#library type i.e. sanger (default) or illumina 
       --lib sanger
#print flag options to stdout
       --help  

References

1. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2010;38(6):1767–71

2. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998;8(3):175–85.

3. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998;8(3):186–94.

Contributing

All contributions are welcome.

Support

If you have any problem or suggestion please open an issue here.

License

GNU GENERAL PUBLIC LICENSE