CD-HIT(1)

💖 NAME 💖

cd-hit — ok so basically it groups sequences together, fast, and it's lowkey iconic for it 🧬✨

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🌸 SYNOPSIS 🌸

cd-hit [Options]

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🦋 DESCRIPTION 🦋

====== CD-HIT version 4.8.1 (built on Aug 20 2021) ======

Bestie, that's the version banner, and it's giving "I was built on Aug 20 2021 and I have been slaying ever since." 💅

Now. The options. There are a LOT of them. Grab a snack. 🍓

✨ Options ✨

• -i — the input filename, in fasta format. This one is required, no skipping it. It can also be in .gz format, so go off compressed files. 🫶
• -o — the output filename. Also required. You literally cannot do this without it.
• -c — the sequence identity threshold, default 0.9. This is cd-hit's default "global sequence identity", and here's the math: number of identical amino acids or bases in the alignment divided by the full length of the shorter sequence. That's the whole vibe.
• -G — use global sequence identity, default 1. If you set it to 0, it uses local sequence identity instead, which is calculated as: number of identical amino acids or bases in the alignment divided by the length of the alignment. > ⚠️ NOTE!!! do not use -G 0 unless you also use alignment coverage controls — see options -aL, -AL, -aS, -AS. Do not play with this one unsupervised, fr fr. 😭
• -b — band_width of alignment, default 20.
• -M — memory limit in MB for the program, default 800; 0 means unlimitted (that spelling is theirs, we respect it 💀).
• -T — number of threads, default 1; with 0, all CPUs will be used. Go parallel, queen. 🔥
• -n — word_length, default 5. See the user's guide for how to choose it. 👑
• -l — length of throw_away_sequences, default 10.
• -t — tolerance for redundance, default 2.
• -d — length of description in the .clstr file, default 20. If you set it to 0, it takes the fasta defline and stops at the first space.
• -s — length difference cutoff, default 0.0. If you set it to 0.9, the shorter sequences need to be at least 90% the length of the representative of the cluster.
• -S — length difference cutoff in amino acid, default 999999. If you set it to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60.
• -aL — alignment coverage for the longer sequence, default 0.0. If you set it to 0.9, the alignment must cover 90% of the sequence.
• -AL — alignment coverage control for the longer sequence, default 99999999. If you set it to 60 and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues.
• -aS — alignment coverage for the shorter sequence, default 0.0. If you set it to 0.9, the alignment must cover 90% of the sequence.
• -AS — alignment coverage control for the shorter sequence, default 99999999. If you set it to 60 and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues.
• -A — minimal alignment coverage control for both sequences, default 0. The alignment must cover >= this value for both sequences.
• -uL — maximum unmatched percentage for the longer sequence, default 1.0. If you set it to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence.
• -uS — maximum unmatched percentage for the shorter sequence, default 1.0. If you set it to 0.1, the unmatched region (excluding leading and tailing gaps) must not be more than 10% of the sequence.
• -U — maximum unmatched length, default 99999999. If you set it to 10, the unmatched region (excluding leading and tailing gaps) must not be more than 10 bases.
• -B — 1 or 0, default 0. By default, sequences are stored in RAM; if set to 1, sequences are stored on hard drive. > 💀 !! No longer supported !! Yeah. RIP to that one, bestie. Do not come for her, she's retired.
• -p — 1 or 0, default 0. If set to 1, print alignment overlap in the .clstr file.
• -g — 1 or 0, default 0. With cd-hit's default algorithm, a sequence is clustered to the first cluster that meets the threshold (fast cluster). If set to 1, the program will cluster it into the most similar cluster that meets the threshold (accurate but slow mode). But either 1 or 0 won't change the representatives of the final clusters — that part stays the same, no cap. 🎀
• -sc — sort clusters by size (number of sequences), default 0. If set to 1, output clusters by decreasing size. (Default 0 outputs clusters by decreasing length.)
• -sf — sort fasta/fastq by cluster size (number of sequences), default 0, no sorting. If set to 1, output sequences by decreasing cluster size. > ⚠️ Heads up: this can be very slow if the input is in .gz format. Like, go get a beverage slow. 😭
• -bak — write backup cluster file (1 or 0, default 0).
• -h — print this help. The classic. The icon. 👑

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🌈 QUESTIONS, BUGS, AND OTHER BUSINESS 🌈

Questions, bugs, contact Weizhong Li at liwz@sdsc.edu

For updated versions and information, please visit: http://cd-hit.org

or https://github.com/weizhongli/cdhit

cd-hit web server is also available from http://cd-hit.org

If you find cd-hit useful, please kindly cite:

"CD-HIT: a fast program for clustering and comparing large sets
of protein or nucleotide sequences", Weizhong Li & Adam Godzik.
Bioinformatics, (2006) 22:1658-1659
"CD-HIT: accelerated for clustering the next generation
sequencing data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu
& Weizhong Li. Bioinformatics, (2012) 28:3150-3152

🫶 Real talk: if this tool carried your research, cite the authors. It's free, it takes ten seconds, and it's the polite thing to do. Periodt.

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And that's the whole page, bestie. This one's cd-hit 4.8.1, from August 2021, and it lives in the CD-HIT(1) section of your manual. Go cluster something gorgeous. 🦋✨💖