Difference between revisions of "Clustering of reads"
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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: | 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: | ||
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wget https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-linux-x86_64 | wget https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-linux-x86_64 | ||
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./vsearch-1.1.3-linux-x86_64 | ./vsearch-1.1.3-linux-x86_64 | ||
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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. | 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. | ||
Latest revision as of 14:02, 24 August 2015
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.
