NAME

       qualityScores - toolkit for processing next-gen sequencing data

DESCRIPTION

       qualityScore Version 2.0.4

              Retrieve Phred score for read bases

       Usage:

              ./qualityScores [options] -i <input_file> -o <output_file>

       Required arguments:

       -i <string>
              Name of input file including read data. The default format is Fastq.

       -o <string>
              Name of output file that is a text file including Phred scores for each read base.

       Optional arguments:

       --gzFASTQinput Input file is in gzipped Fastq format.

       --BAMinput
              Input file is in BAM format.

       --SAMinput
              Input file is in SAM format.

       --first-end
              Use only first reads in paired-end data. Only applicable for paired-end BAM/SAM input.

       --second-end
              Use only second reads in paired-end data. Only applicable for paired-end BAM/SAM input.

       --counted-reads <int> Total number of reads to be extracted from the input

              file. 10,000 by default.

       --phred-offset <33|64> refer to subread aligner.

AUTHOR

        This manpage was written by Alexandre Mestiashvili for the Debian distribution and
        can be used for any other usage of the program.

qualityScores 2.0.3                                March 2023                                   QUALITYSCORES(1)