CD-HIT-2D(1)

💖 CD-HIT-2D 💖

okay bestie, so you found the cd-hit-2d manpage and honestly? this little icon is about to group your sequences and it does it fast. sit down, grab a strawberry 🍓, and let's get into it.

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✨ NAME ✨

cd-hit-2d — quickly group sequences in db1 or db2 format. yes that's literally the whole vibe. grouping. speed. slay. 💅

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✨ SYNOPSIS ✨

cd-hit-2d [Options]

that's it. that's the whole call. just you, your options, and destiny. 🦋

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✨ DESCRIPTION ✨

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

that's the version banner, no cap — this is CD-HIT version 4.8.1, built on Aug 20 2021. ✨

🎀 Options 🎀

okay here comes the main character section. every single flag, nothing skipped, i would never do you like that. 💜

• -i — input filename for db1 in fasta format, required, and yes it can be in .gz format. compressed queens stay winning. 🫶
• -i2 — input filename for db2 in fasta format, required, and also can be in .gz format. two dbs, one dream. 🦋
• -o — output filename, required. like obviously bestie, where else is it gonna go 😭
• -c — sequence identity threshold, default 0.9. this is the default cd-hit's "global sequence identity", calculated as: number of identical amino acids or bases in alignment divided by the full length of the shorter sequence. math but make it fashion. ✨
• -G — use global sequence identity, default 1. if you set it to 0, then it uses local sequence identity, calculated as: number of identical amino acids or bases in alignment divided by the length of the alignment.

NOTE!!! don't use -G 0 unless you use alignment coverage controls — see options -aL, -AL, -aS, -AS. i'm serious bestie, i'm not being dramatic, this one matters. 💀

• -b — band_width of alignment, default 20.
• -M — memory limit (in MB) for the program, default 800; 0 for unlimitted; (their spelling, not mine, i'm just the messenger 🎀).
• -T — number of threads, default 1; with 0, all CPUs will be used. multitasking queen energy 👑
• -n — word_length, default 5, see user's guide for choosing it. iykyk. 📖
• -l — length of throw_away_sequences, default 10. bye girl, you're too short 🚮
• -t — tolerance for redundance, default 2.
• -d — length of description in .clstr file, default 20. if set to 0, it takes the fasta defline and stops at first space. ✂️
• -s — length difference cutoff, default 0.0. if set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster.
• -S — length difference cutoff in amino acid, default 999999. if set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60.
• -s2 — length difference cutoff for db1, default 1.0. by default, seqs in db1 >= seqs in db2 in a same cluster. if set to 0.9, seqs in db1 may just >= 90% seqs in db2.
• -S2 — length difference cutoff, default 0. by default, seqs in db1 >= seqs in db2 in a same cluster. if set to 60, seqs in db2 may 60aa longer than seqs in db1.
• -aL — alignment coverage for the longer sequence, default 0.0. if set to 0.9, the alignment must covers 90% of the sequence.
• -AL — alignment coverage control for the longer sequence, default 99999999. if set 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 set to 0.9, the alignment must covers 90% of the sequence.
• -AS — alignment coverage control for the shorter sequence, default 99999999. if set 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 the both sequences, default 0. alignment must cover >= this value for both sequences. equal treatment for everybody, we love to see it 🌈
• -uL — maximum unmatched percentage for the longer sequence, default 1.0. if set 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 set 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 set 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, sequence are stored on hard drive.

!! No longer supported !! 🪦 rip, she's retired, do not come for her.

• -p — 1 or 0, default 0. if set to 1, print alignment overlap in .clstr file. receipts on receipts 🧾✨
• -g — 1 or 0, default 0. by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast cluster). if set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode). but either 1 or 0 won't change the representatives of final clusters. so pick your vibe: fast or thorough 🏃♀️💨 vs 🐢
• -bak — write backup cluster file (1 or 0, default 0). safety first bestie 💾
• -h — print this help. the classic. the legend. 🙌

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🌸 CONTACT & CITATION 🌸

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

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

cite the queens that built the thing, it's literally the least we can do 🫶📚

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🦋 SEE ALSO 🦋

nothing listed here in this one bestie — but you already know where to find the rest of the cd-hit family. 👀

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and that's the whole page!! ✨💖✨ this was cd-hit-2d version 4.8.1, dated August 2021 — that's the source/version and date, tucked right here in the sign-off like a lil bow on top 🎀 go cluster something gorgeous, bestie, you've got this 💅🌟💜