CD-HIT-EST-2D(1)

💖 CD-HIT-EST-2D 💖

okay so bestie, welcome to the manual page for cd-hit-est-2d (that's section 1 of the manuals, for the record 👑). It runs the CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format. Yes, that's the whole vibe. Let's get into it 💅

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✨ SYNOPSIS ✨

cd-hit-est-2d [Options]

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🌸 DESCRIPTION 🌸

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

That's literally the build, no cap. Now the options, and there are a LOT of them, so buckle up 🎀

🦋 Options 🦋

• -i — input filename for db1 in fasta format, required, can be in .gz format
• -i2 — input filename for db2 in fasta format, required, can be in .gz format
• -j, -j2 — input filename in fasta/fastq format for R2 reads if your input are paired end (PE) files
• -i db1-R1.fq -j db1-R2.fq -i2 db2-R1.fq -j2 db2-R2.fq -o output_R1 -op output_R2 — or
• -i db1-R1.fa -j db1-R2.fa -i2 db2-R1.fq -j2 db2-R2.fq -o output_R1 -op output_R2
• -o — output filename, required
• -op — output filename for R2 reads if your input are paired end (PE) files
• -c — sequence identity threshold, default 0.9. This is the default cd-hit "global sequence identity", calculated as: number of identical amino acids or bases in alignment divided by the full length of the shorter sequence
• -G — use global sequence identity, default 1. If set to 0, then use 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

• -b — band_width of alignment, default 20
• -M — memory limit (in MB) for the program, default 800; 0 for unlimitted;
• -T — number of threads, default 1; with 0, all CPUs will be used
• -n — word_length, default 10, see user's guide for choosing it
• -l — length of throw_away_sequences, default 10
• -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
• -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 !! 💀

• -P — input paired end (PE) reads, default 0, single file. If set to 1, please use -i R1 -j R2 to input both PE files
• -cx — length to keep after trimming the tail of sequence, default 0, not trimming. If set to 50, the program only uses the first 50 letters of input sequence
• -cy — length to keep after trimming the tail of R2 sequence, default 0, not trimming. If set to 50, the program only uses the first 50 letters of input R2 sequence, e.g. -cx 100 -cy 80 for paired end reads
• -p — 1 or 0, default 0. If set to 1, print alignment overlap in .clstr file
• -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
• -r — 1 or 0, default 1. By default do both +/+ & +/- alignments. If set to 0, only +/+ strand alignment
• -mask — masking letters (e.g. -mask NX, to mask out both 'N' and 'X')
• -match — matching score, default 2 (1 for T-U and N-N)
• -mismatch — mismatching score, default -2
• -gap — gap opening score, default -6
• -gap-ext — gap extension score, default -1
• -bak — write backup cluster file (1 or 0, default 0)
• -h — print this help

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💌 Questions, bugs, contact 💌

Got questions? Bugs? Wanna slide into the DMs? Contact Weizhong Li at liwz@sdsc.edu 🫶

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

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

The 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

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and that's the whole page bestie 🎀 cd-hit-est-2d is sitting at version 4.8.1, this manual page is dated August 2021, and you just read CD-HIT-EST-2D(1). slay, go cluster something 💅✨👑