Analysis of CD-HIT and comparisons with USEARCH
I am sometimes asked about CD-HIT and how CD-HIT clustering compares
with the UCLUST algorithm in USEARCH. Below are links to pages
discussing issues around CD-HIT and assessment of clustering methods.
Different methods report different pair-wise identities
Example where CD-HIT id is 97% and USEARCH id is 86%
Example where CD-HIT id is 97% and USEARCH id is 95%
CD-HIT alignment errors due to banding
CD-HIT reports systematically higher %ids compared to USEARCH
CD-HIT has low gap penalties and mismatch scores
CD-HIT v4 and USEARCH v5 results on 16S rRNA reads from Costello et al.