LIGHTER(1)

✨ lighter(1) — the sequencing error corrector that actually respects your RAM ✨

okay bestie, gather round 💖 this is the manual page for lighter, a User Command that fixes sequencing errors and does it fast and cheap on memory. she's that girl. no cap.

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🌸 NAME 🌸

lighter — fast and memory-efficient sequencing error corrector

like literally, that's the whole vibe: correcting sequencing errors without making your computer cry. 🫶

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🎀 SYNOPSIS 🎀

lighter [OPTIONS]

that's it. that's the whole thing. you feed her options, she eats them. periodt. 💅

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🦋 DESCRIPTION 🦋

so here's the tea ☕ Lighter is a fast, memory-efficient tool for correcting sequencing errors. and the way she does it is genuinely iconic:

Lighter avoids counting k-mers. instead?? she uses a pair of Bloom filters — one holding a sample of the input k-mers, and the other holding k-mers likely to be correct. yes, two. a whole duo. main character energy fr fr. ✨

and the trick?? as long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, the Bloom filter size can be held constant while maintaining near-constant accuracy. like, she doesn't balloon up when your data gets deep. she stays chill. 💅

Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy. not me being obsessed with an error corrector 😭

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✨ OPTIONS: ✨

💖 Required parameters:

these ones? not optional. she needs them. don't skip them bestie.

• -r seq_file — seq_file is the path to the sequence file. you can use multiple -r to specify multiple sequence files 🫶

the file can be fasta and fastq, and can be gzip'ed with extension *.gz. and when the input file is *.gz, the corresponding output file will also be gzip'ed. matching energy. iconic.

• -k kmer_length genome_size alpha — (see README for information on setting alpha) 📖

or

• -K kmer_length genom_size — in this case, the genome size should be relative accurate. like, actually accurate. don't be sloppy with this one. 🙈

🌈 Other parameters:

• -od output_file_directory — (default: ./) 📁
• -t num_of_threads — number of threads to use (default: 1) 🧵 go wild, she's parallelized
• -maxcor INT — the maximum number of corrections within a 20bp window (default: 4)
• -trim — allow trimming (default: false) ✂️
• -discard — discard unfixable reads. Will LOSE paired-end matching when discarding (default: false) 💀

bestie. read that again. you will LOSE your paired-end matching. she said what she said. be careful.

• -noQual — ignore the quality socre (default: false) 🙈 yes, "socre". we keep it exactly as written. character for character. that's the rule. 💅
• -newQual ascii_quality_score — set the quality for the bases corrected to the specified score (default: not used) ⭐
• -saveTrustedKmers file — save the trusted kmers to specified file then stop (default: not used) 🛑
• -loadTrustedKmers file — directly get solid kmers from specified file (default: not used) 📥
• -zlib compress_level — set the compression level(0-9) of gzip (default: 1) 🗜️
• -h — print the help message and quit 🆘
• -v — print the version information and quit 👑

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💜 AUTHOR 💜

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

shoutout to Andreas, the realest 🫶

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and that's the whole page bestie!! you're now fully literate in lighter(1). go correct some errors, slay, and remember: sampling fraction in inverse proportion to sequencing depth. iykyk 💅✨

lighter version 1.1.2, from May 2020. mwah, love u, bye 🎀🦋💖