HPC-CLUST statistics

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HPC-CLUST specifications

Information


Unique identifier OMICS_01446
Name HPC-CLUST
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A set of pre-aligned sequences
Operating system Unix/Linux
Programming languages C++
Parallelization MPI
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline C. von Mering <>

Publication for HPC-CLUST

HPC-CLUST in publications

 (3)
PMCID: 5705695
PMID: 29184071
DOI: 10.1038/s41598-017-16287-4

[…] did not align to the model or were not classified as bacterial by mapseq, reads were pre-clustered (one mismatch abundance-sorted single linkage) and then hierarchically clustered into otus using hpc-clust according to the average linkage algorithm which has previously been shown to provide reproducible and consistent clustering. otu sets were generated at different levels of sequence […]

PMCID: 5322292
PMID: 27935587
DOI: 10.1038/ismej.2016.139

[…] secondary structure-aware 16s rrna model using infernal (), denoised by a global minimum read abundance at 1% tolerance of 4 and clustered into otus at 97% average linkage sequence similarity using hpc-clust (), as established previously (, ). the resulting filtered taxa count table contained 24 717 447 sequences clustered into 27 041 otus across 3849 samples. a phylogenetic tree of otu […]

PMCID: 3998914
PMID: 24763141
DOI: 10.1371/journal.pcbi.1003594

[…] software with the cluster_fast option and standard parameters. hierarchical average, complete and single linkage clustering were implemented using the recently developed in-house software package hpc-clust using the ‘onegap’ sequence distance calculator (counting gaps as single mismatches). hpc-clust parallelizes the hierarchical clustering task and has been shown to cluster sequences […]


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HPC-CLUST institution(s)
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
HPC-CLUST funding source(s)
ERC grant (Starting Grant ‘UMICIS/242870’)

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