pku-embl/metagenomics-skills/cd-hit

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

set -Eeuo pipefail
genes="${1:?usage: cluster-genes.sh GENES_FNA OUTPUT_DIR}"
out="${2:?usage: cluster-genes.sh GENES_FNA OUTPUT_DIR}"
threads="${THREADS:-8}"
memory_mb="${MEMORY_MB:-0}"
test -s "$genes" || exit 2
test ! -e "$out" || { echo "use a new output directory: $out" >&2; exit 2; }
mkdir -p "$out"
 
cd-hit-est -i "$genes" -o "$out/nucleotide.fa" \
  -aS 0.9 -c 0.95 -G 0 -g 0 -T "$threads" -M "$memory_mb" \
  >"$out/cd-hit.stdout.log" 2>"$out/cd-hit.stderr.log"
test -s "$out/nucleotide.fa"
test -s "$out/nucleotide.fa.clstr"
seqkit translate --trim "$out/nucleotide.fa" \
  >"$out/protein.fa" 2>"$out/translate.stderr.log"

Validation, recovery, and provenance

Verify unique representative IDs, cluster membership coverage, sequence counts before/after, length/partial-gene distributions, and nucleotide-to-protein ID mapping. Test threshold sensitivity when catalogue richness is a result. The common 95% identity/90% shorter-sequence coverage policy defines an operational gene family; it is not a universal orthology boundary.

Use a new output after changing input order or clustering thresholds. Record CD-HIT/SeqKit versions, input checksum, identity/coverage/global-local settings, threads/memory, commands, logs, representative and .clstr checksums, and cluster statistics.

Related skills

prodigal · salmon · eggnog-mapper · mmseqs2