CD-Hit

CD-HIT is a sequence clustering tool used to remove redundancy from protein or nucleotide sequence sets. In this module, predicted ORF protein sequences are clustered to build a non-redundant gene catalog.

Workflow

1. Input predicted ORF sequences
   Upload ORF amino acid files (.faa) and matching nucleotide files (.ffn) generated from gene prediction.

2. Merge sample sequences
   Combine ORF sequences from all samples and add sample labels to sequence IDs to avoid duplicate identifiers.

3. Cluster protein sequences
   Run CD-HIT with identity and coverage thresholds to group highly similar protein sequences.

4. Select representative genes
   Extract representative protein sequences from each cluster and retrieve the corresponding nucleotide sequences.

5. Generate gene catalog summary
   Output the non-redundant protein catalog, nucleotide gene catalog, and summary statistics such as input ORFs and cluster counts.

Data

The CD-HIT sample dataset contains predicted ORF sequences from a single sample, sampleA, including amino acid sequences (sampleA.orf_100nt.faa) and corresponding nucleotide sequences (sampleA.orf_100nt.ffn). These sequences are used to demonstrate redundancy removal and representative gene catalog construction by CD-HIT clustering.

Result

v0.4: The pipeline is stored in Code Repository: CRS1234651212603994112. The computational docker enrionment is stored in Software Repository: SRS1234669566765051904.

Reproducibility

The pipeline utilizes code CRS1225977902999547904 and Docker image SRS1225987480378159104, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'CD-Hit'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.