cd-hit

name	cd-hit
description	Cluster genes/proteins to build non-redundant catalogues. Use this skill when working with cd-hit: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/weizhongli/cdhit. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["clustering","dereplication"]
upstream	https://github.com/weizhongli/cdhit

CD-HIT

Upstream: weizhongli/cdhit

Citation

Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012). https://doi.org/10.1093/bioinformatics/bts565

See also docs/references.md.

Analytical thinking

cd-hit-est collapses redundant nucleotide ORFs into a non-redundant catalogue. Defaults used widely in shotgun catalogues: identity 0.95, alignment coverage 0.9 (-c 0.95 -aS 0.9). Changing thresholds changes biological interpretation of “a gene”—report them.

How to run

cd-hit-est -i genes.fna -o NR/nucleotide.fa \
  -aS 0.9 -c 0.95 -G 0 -g 0 -T 0 -M 0
seqkit translate --trim NR/nucleotide.fa > NR/protein.fa

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