FILTLONG(1)

💖 FILTLONG(1) 💖

okay so bestie, listen — filtlong is a quality filtering tool for Nanopore and PacBio reads and it is genuinely the moment. long reads? filtered. mid reads? gone. we're keeping only the good ones. periodt. 💅

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✨ NAME ✨

filtlong — quality filtering tool for Nanopore and PacBio reads 🦋

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🌸 SYNOPSIS 🌸

filtlong {OPTIONS} [input_reads]

that's it. that's the whole vibe. options go in, reads come out, everyone's thriving. ✨

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👑 OPTIONS 👑

🎀 positional arguments:

• input_reads — the long reads you want filtered, bestie. hand them over. 🫶

💅 optional arguments:

⭐ output thresholds:

• -t[int], --target_bases [int] — keep only the best reads, up until you've hit this many total bases. that's the cap, no cap. 🔥
• -p[float], --keep_percent [float] — keep only this percentage of the best reads (measured by bases, so it's a base girlie not a count girlie). 💖
• --min_length [int] — the minimum length threshold, fr fr. anything shorter? not invited. 🙈
• --min_mean_q [float] — minimum mean quality threshold. 🎀
• --min_window_q [float] — minimum window quality threshold. 🌸

🌈 external references (if provided, read quality will be determined using these instead of from the Phred scores):

like, if you hand it a reference, it's gonna judge your reads against that instead of the Phred scores. iykyk. 👑

• -a[file], --assembly [file] — reference assembly in FASTA format. 🧚
• -1[file], --illumina_1 [file] — reference Illumina reads in FASTQ format. 💜
• -2[file], --illumina_2 [file] — reference Illumina reads in FASTQ format. 💜

🦋 score weights (control the relative contribution of each score to the final read score):

these three lil weights decide how much each score pulls up to the final read score. balance them like your life depends on it (it doesn't, but still). ✨

• --length_weight [float] — weight given to the length score (default: 1). 📏
• --mean_q_weight [float] — weight given to the mean quality score (default: 1). 💯
• --window_q_weight [float] — weight given to the window quality score (default: 1). 🪟

💀 read manipulation:

• --trim — trim non-k-mer-matching bases from the start/end of reads. literally trimming the edges off. slay. ✂️
• --split [split] — split reads at this many (or more) consecutive non-k-mer-matching bases. cutting the read into pieces, main character energy. 🔪

🌟 other:

• --window_size [int] — size of the sliding window used when measuring window quality (default: 250). 🪟✨
• --verbose — verbose output to stderr with info for each read. not me being nosy about every single read. 😭
• --version — display the program version and quit. 💅
• -h, --help — display this help menu. the classic. 🎀

for more information, go to: https://github.com/rrwick/Filtlong — go go go, bestie. 🫶

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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. iconic of them honestly. 👑

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and that's the whole thing!! this is filtlong version 0.2.0, dated January 2019 — shoutout to the Debian fam for shipping it, we're obsessed. 💖✨🎀 bye bestie, go filter some reads 🦋🌸