CD-HIT-454(1)

💖 NAME 💖

cd-hit-454 — quickly group sequences, optimised for 454 data 🦋

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✨ SYNOPSIS ✨

cd-hit-454 [Options]

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🎀 DESCRIPTION 🎀

okay bestie, first thing you see when you run this is the little banner flexing its whole build identity, and honestly? iconic:

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

💅 Options 💅

• -i — input filename in fasta format, and yes it's required. Can be in .gz format too, we love a compressed queen 🫶
• -o — output filename, also required, no you cannot skip it
• -c — sequence identity threshold, default 0.98. This is a "global sequence identity" and it's calculated as: number of identical amino acids or bases in the alignment divided by the full length of the shorter sequence + gaps ✨
• -b — band_width of the alignment, default 10
• -M — memory limit in MB for the program, default 800; set it to 0 for unlimited 👑
• -T — number of threads, default 1; if you set it to 0, all CPUs will be used 🔥
• -n — word_length, default 10, and bestie if you're wondering how to pick it, go read the user's guide, it's giving required reading 📖
• -aL — alignment coverage for the longer sequence, default 0.0. Set it to 0.9 and the alignment must cover 90% of the sequence 💅
• -AL — alignment coverage control for the longer sequence, default 99999999. So if you set it to 60 and the length of the sequence is 400, then the alignment must be >= 340 (400-60) residues, math ate that 🧮
• -aS — alignment coverage for the shorter sequence, default 0.0. Set it to 0.9 and 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, same energy as its longer-sequence sibling 🧮
• -B — 1 or 0, default 0. By default sequences are stored in RAM; set it to 1 and sequences are stored on the hard drive.

😭 !! No longer supported !! do not come for me, I'm just the messenger

• -g — 1 or 0, default 0. With cd-hit's default algorithm, a sequence gets clustered to the first cluster that meets the threshold (fast cluster). Set it to 1 and the program clusters it into the most similar cluster that meets the threshold (accurate but slow mode). But lowkey, either 1 or 0 won't change the representatives of the final clusters, so don't stress 🌸
• -D — max size per indel, default 1
• -match — matching score, default 2
• -mismatch — mismatching score, default -1
• -gap — gap opening score, default -3
• -gap-ext — gap extension score, default -1
• -bak — write backup cluster file (1 or 0, default 0)
• -h — print this help, the classic 🎀

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🫶 Questions, bugs, contact 🫶

Got questions? Got bugs? Contact Weizhong Li at liwz@sdsc.edu 📧

And if you find cd-hit useful, please kindly cite these, it's the polite thing to do fr fr:

1. "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
2. "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
3. "Beifang Niu, Limin Fu, Shulei Sun and Weizhong Li. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics (2010) 11:187"

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and that's the whole page bestie, cd-hit-454 version 4.8.1, August 2021, page CD-HIT-454(1) — go cluster something gorgeous 💜🌈⭐