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

https://github.com/torognes/vsearch

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:

wget https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-linux-x86_64

chmod 755 vsearch-1.1.3-linux-x86_64

./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.