What it does
vsearch implements a single-pass, greedy star-clustering algorithm, similar to the algorithms implemented in usearch, DNAclust and sumaclust for example.
--centroids FILENAME | |
output centroid sequences to FASTA file | |
--cluster_fast FILENAME | |
cluster sequences after sorting by length | |
--cluster_size FILENAME | |
cluster sequences after sorting by abundance | |
--cluster_smallmem FILENAME | |
cluster already sorted sequences (see -usersort) | |
--clusters STRING | |
output each cluster to a separate FASTA file | |
--consout FILENAME | |
output cluster consensus sequences to FASTA file | |
--cons_truncate | |
do not ignore terminal gaps in MSA for consensus | |
--id REAL | reject if identity lower |
--iddef INT | id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2) |
--msaout FILENAME | |
output multiple seq. alignments to FASTA file | |
--qmask | seqs with dust, soft or no method (dust) |
--sizein | propagate abundance annotation from input |
--sizeout | write cluster abundances to centroid file |
--strand | cluster using plus or both strands (plus) |
--uc FILENAME | filename for UCLUST-like output |
--usersort | indicate sequences not presorted by length |
For details about this tool, please refer to the GitHub repository or the vsearch manual.