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oclust | Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

Clusters long 16S rRNA sequencing reads, or any sequences, into Operational Taxonomic Units. oclust permits the reduction of computational footprint (sequences can be aligned within reasonable time and memory on a desktop computer) as well as the incorporation of secondary structure information in the alignment. For better performance, complete-linkage is the default choice for oclust. It provides the most ecologically consistent partition of 16S data

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oclust classification

oclust specifications

Unique identifier:
OMICS_15061
Interface:
Command line interface
Input format:
FASTA
Programming languages:
Perl
Stability:
Stable
Software type:
Pipeline/Workflow
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes

oclust distribution

versioning

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oclust support

Documentation

Maintainer

  • Ali Bashir <>

Credits

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Publications

Institution(s)

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA

Funding source(s)

This work was funded by NIDDK: 1K01DK094986-01, New York Crohn’s Foundation, and the Chemotherapy Foundation.

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