QUALITYSCORES(1)

✨ NAME ✨

qualityScores — bestie, it's a whole toolkit for processing next-gen sequencing data 💖

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🦋 DESCRIPTION 🦋

okay so this is qualityScore Version 2.0.4, and its entire job — its main character moment — is retrieving the Phred score for read bases. literally that's it, that's the gig 💅

Usage:

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

🎀 Required arguments 🎀

these are not optional, bestie, you cannot skip them, the program will simply not be slaying without them 😭

• -i <string> — the name of the input file, aka the one holding your read data. the default format is Fastq. 🧚
• -o <string> — the name of the output file, which is a text file holding the Phred scores for each read base. yes, every single base. she's thorough. 👑

🌸 Optional arguments 🌸

mix and match as your little heart desires 🫶

• --gzFASTQinput — tells it your input file is in gzipped Fastq format. zipped up and cute. ✨
• --BAMinput — input file is in BAM format.
• --SAMinput — input file is in SAM format.
• --first-end — use only the first reads in paired-end data. heads up: this is only applicable for paired-end BAM/SAM input, so don't come for her if you're using Fastq. 🙈
• --second-end — use only the second reads in paired-end data. same deal: only applicable for paired-end BAM/SAM input.
• --counted-reads <int> — total number of reads to be extracted from the input file. it's 10,000 by default, so if you wanted a different number, speak now. 🔥
• --phred-offset <33|64> — refer to subread aligner. (that's the whole description, bestie, iykyk — she's keeping it mysterious 💀)

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💜 AUTHOR 💜

this manpage was written by Alexandre Mestiashvili for the Debian distribution, and can be used for any other usage of the program. shoutout to the author, absolute icon, no cap 🫶👑

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and that's the whole page, bestie!! this was qualityScores 2.0.3, from March 2023, and honestly? she ate. 💅🌸⭐