Clustering of reads

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Qiime does not contain an internal clustering algorithm. Rather, an external program must be specified; Qiime will send the data to be clustered to the sepcified program and subsequently import the clusters back into Qiime.

Here, the user might experience problems if using high-volume sequencing data. The free 32-bit version of the USEARCH algorithm often as the external algorithm cannot deal with massive sequencing data (the USEARCH 64-bit version is not free and is not installed on Abel).

The vsearch program may be used for clustering instead. See

for information about this algorithm. This program is not installed on Abel; to use it, download it and grant executive permission to the program. Execute the program without arguments to display the usage information:


chmod 755 vsearch-1.1.3-linux-x86_64


The latest version of Qiime (v1.9.1) allows the usage of the SWARM algorithm instead of USEARCH. This program, however, is not installed on Abel yet.