fastQ_brew v.1.0.4

• [x] Filters FASTQ reads
• [x] Only uses Perl core
• [x] Platform independent
• [x] Fast and easy to use
• [x] Removes duplicate reads
• [x] Trims reads by length or quality
• [x] Returns summary statistics
• [x] Removes specific adapters
• [x] Implements a fast mismatch algorithm for adapter removal
• [x] Performs various file conversions

Installation

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

Usage

Type the following to run:

 #brew_driver.pl is a driver script within the lib folder 
 
 perl brew_driver.pl -i=<input_file> -path=./ -qf=30 -adpt_r=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -mis_r=1 -smry -dup -no_n -clean 
 
 #see below for command flags 

view standard adapters here

Command Line Arguments

Filtering Options

#filter by read quality
       -qf=30
#filter by read length       
       -lf=25
#remove x bases from left 
       -trim_l=5
#remove x bases from right
       -trim_r=3
#remove specified adapter from left
       -adpt_l="AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
#remove sequences from left end that match specified 
#adapter but have x number of mismatches
       -mis_l=1
#remove specified adapter from right
       -adpt_r="AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
#remove sequences from right end that match specified 
#adapter but have x number of mismatches
       -mis_r=2
#remove duplicate reads 
       -dup

File Conversions

#convert FASTQ file to FASTA format file
       -fasta
#convert the DNA to RNA 
       -rna
#reverse complement the FASTQ reads 
       -rev_comp

Odds and Ends

#input FASTQ file (required) 
       -i=reads.fastq
#path to FASTQ file (defaults to cwd) 
       -path=./ 
#library type i.e. sanger (default) or illumina 
       -lib=sanger
#return summary statistics on unfiltered and filtered data 
       -smry     
#remove reads that contain non designated bases e.g. N 
       -no_n
#remove temporary files generated during the run
       -clean  
#print flag options to STDOUT
       -help  

Contributing

All contributions are welcome.

Support

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

License

GNU GENERAL PUBLIC LICENSE