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.