---
name: "qualityScores"
section: "1"
platform: "linux"
package: "subread"
version: "2.0.8+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/qualityScores"
---

# qualityScores(1)

toolkit for processing next-gen sequencing data

## 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.