fastQ_brew ver 1.0.2

Damien O'Halloran, The George Washington University, 2017

Filter FASTQ reads

Installation

1. Download and extract the fastQ_brew.zip file
   tar -xzvf fatsQ_brew.zip
2. The extracted dir will be called fastQ_brew
   cd fastQ_brew
perl Makefile.PL
make
make test
make install

Usage

Run as follows:

 use fastQ_brew;
 use List::Util qw(min max sum);
 use fastQ_brew_Utilities;
 use Cwd;
 
 my $lib       = "sanger";
 my $file_path = cwd();
 my $in_file   = "sample_sanger.fastq";

 my $tmp = fastQ_brew->new();

 $tmp->load_fastQ_brew(
                   library_type  => $lib || "illumina",
                   file_path     => $file_path,
                   in_file       => $in_file,
                   qual_filter   => 1200,
                   length_filter => 80
 );

 $tmp->run_fastQ_brew();

Filtering Options

#filter by read quality
       qual_filter   => 1200
#filter by read length       
       length_filter => 45
#remove x bases from left 
       left_trim     => 5
#remove x bases from right
       right_trim    => 3
#remove specified adapter from left
       adapter_left  => "GTACGTGTGGTGGGGAT"
#remove sequences from left end that match specified 
#adapter but have x number of mismatches
       mismatches_l  => 1
#remove specified adapter from right
       adapter_right  => "GTACGTGTGGTGGGGAT"
#remove sequences from right end that match specified 
#adapter but have x number of mismatches
       mismatches_r  => 2
#remove duplicate reads
       de_duplex     => "Y"

File Conversions

#convert FASTQ file to FASTA format file
       fasta_convert => "Y"
#convert the DNA to RNA 
       dna_rna       => "Y"
#reverse complement the FASTQ reads 
       rev_comp      => "Y"
#remove temporary files generated during the run
       cleanup       => "Y"

Odds and Ends

#remove reads that contain non designated bases e.g. N 
       remove_n      => "Y"
#remove temporary files generated during the run
       cleanup       => "Y"

Contributing

All contributions are welcome.

Support

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

License

GNU GENERAL PUBLIC LICENSE