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ADEPT, a dynamic next generation sequencing data error-detection program with trimming

======= ADEPT is a program that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution for the dataset being analyzed.

PREREQUISITES

  1. The main program is developed in Perl v 5.8.8.
  2. Parallel::ForkManager module from CPAN
    (http://search.cpan.org/~dlux/Parallel-ForkManager-0.7.9/lib/Parallel/ForkManager.pm)
  3. String::Approx module from CPAN
    (http://search.cpan.org/~jhi/String-Approx-3.27/Approx.pm)
  4. R for ploting
    (http://www.r-project.org/)

BASIC USAGE

  • Trimming by quality 5 and filtering reads with any ambiguous base or low complexity.

    $ perl ADEPT.pl -p 'reads1.fastq reads2.fastq' -d out_directory

Full USAGE

 perl ADEPT.pl [options] [-u unpaired.fastq] -p 'reads1.fastq reads2.fastq' -d out_directory
 
 Input File: (can use more than once fastq file)
        -u             Unpaired reads
        
        -p             Paired reads in two files and separate by space in quote
 Trim:
        -qE            5" and 3" ends triming # as quality level (0-40) (default 5) for trimming
        -qC            threhold to call a base to be correct (0-1.0) (default = 0.25, higher quality
                       than 25% the nucleotides at that position within the sampled run )
        -qW            threhold to identifying a nucleotide as an error if it falls below a defined 
                       percentage of the quality scores for that position (0-1.0) (default = 0)
        -qMN           ratio of the of the base quality to the qualities of upstream and downstream positions (0-1.0)
                       By default, all qIN ratios must be at least 0.4 to be considered as a potential erroneous base 
                       (i.e. all adjacent qualities must be at least 2.5 times higher than the quality of the position being investigated).
        -qNS           threhold to identify a nucleotide as an potential error if its neighbors' quality falls below a defined 
                       percentage of the quality scores for that neighbors' position within the sampled run (0-1.0) (default = 0.3)

 Filters:
        -min_L         Trimmed sequence length will have at least minimum length (default:50)
        

        					
 Q_Format:
        -ascii         Encoding type: 33 or 64 or autoCheck (default)
                       Type of ASCII encoding: 33 (standard) or 64 (illumina 1.3+)

        -out_ascii     Output encoding. (default: 33)
 Output:
        -prefix        Output file prefix. (default: QC)

        -stats         Statistical numbers output file (default: prefix.stats.txt)

        -d             Output directory.
 Options:
        -t             # of CPUs to run the script (default:2 )

        -split_size    Split the input file into several sub files by sequence number (default: 1000000) 

        -out_non_trim_reads      <bool> Output not trimmed reads to prefix.discard.fastq (default: 0, not output)

        -debug         keep intermediate files

VERSION HISTORY

======== Version 1.1 Stable function release. Features:

  • assesses errors within reads by comparing position-specific and neighboring ba se quality scores with the distribution for the dataset being analyzed.
  • autocheck quality encoding and quality encoding coversion
  • multi-threads (required Parallel::ForkManager)
  • input paired end reads aware

CITATION