SUMACLUST protocols

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SUMACLUST specifications

Information


Unique identifier OMICS_19112
Name SUMACLUST
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 1.0.20
Stability Stable
Source code URL https://git.metabarcoding.org/obitools/sumaclust/uploads/69f757c42f2cd45212c587e87c75a00f/sumaclust_v1.0.20.tar.gz
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Jenya Kopylov <>
  • person_outline Celine Mercier <>

Publication for SUMACLUST

SUMACLUST in pipelines

 (5)
2018
PMCID: 5918560
PMID: 29695307
DOI: 10.1186/s40168-018-0455-y

[…] and otus generated as described previously []; per sample de novo identification and removal of chimeric sequences was undertaken using usearch, and then de novo otus were picked in qiime using sumaclust at a similarity threshold of 97% []. the otu representative sequences were aligned using the parallel_align_seqs_pynast command within qiime, the resulting alignment was then filtered […]

2017
PMCID: 5500185
PMID: 28286339
DOI: 10.1038/ijo.2017.66

[…] basis, discarding paired-ends with an overlap of <200 nt and removing chimeric sequences using de novo chimera detection in usearch. de novo otu clustering was then carried across all reads using sumaclust within qiime 1.9.0, grouping reads with a 97% identity threshold., otu counts were converted to log transformed relative abundances, with zero counts handled by the addition […]

2016
PMCID: 4996804
PMID: 27557607
DOI: 10.1186/s12284-016-0111-8

[…] containing homopolymer stretches longer than 10 bases, ambiguous bases, reads less than 200 bp in length and reads longer than 275 bp using mothur. otu picking was performed using the open reference sumaclust/sortmerna method (kopylova et al. ) as implemented in qiime (pick_open_reference_otus.py). chimeraslayer (haas et al. ) as implemented in mothur was used with the greengenes database […]

2016
PMCID: 5012273
PMID: 27635321
DOI: 10.7717/peerj.2341

[…] clustering and community richness metrics., overall, across previous comparisons of greedy clustering algorithms in combination with the heritability results we have presented here, vsearch and sumaclust seem to produce the best combination of accuracy, stability and heritability. we would therefore recommend either of these approaches for de novo clustering. sumaclust and usearch […]

2016
PMCID: 5069744
PMID: 27832214
DOI: 10.1128/mSystems.00027-16

[…] to the sequence. by choosing to focus on the ability to regenerate taxonomic clusterings, minimizing the number of otus, and computational performance, kopylova et al. () concluded that swarm and sumaclust had the most consistent performance among the de novo methods. my objective mcc-based approach found that sumaclust performed well but was matched or outperformed by the average neighbor […]


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SUMACLUST in publications

 (21)
PMCID: 5931749
PMID: 29732403
DOI: 10.1126/sciadv.aap9661

[…] removed. the reads were then dereplicated using obiuniq, and a chimera removal step was performed using the uchime-denovo algorithm () implemented in vsearch (). the motus were delimited using the sumaclust algorithm () with a constant similarity threshold of 99%. taxonomic assignment of the representative sequences for each motu was performed using the ecotag algorithm (). we built a bespoke […]

PMCID: 5918560
PMID: 29695307
DOI: 10.1186/s40168-018-0455-y

[…] and otus generated as described previously []; per sample de novo identification and removal of chimeric sequences was undertaken using usearch, and then de novo otus were picked in qiime using sumaclust at a similarity threshold of 97% []. the otu representative sequences were aligned using the parallel_align_seqs_pynast command within qiime, the resulting alignment was then filtered […]

PMCID: 5861609
PMID: 29581730
DOI: 10.1186/s13099-018-0239-8

[…] molecules were screened using vsearch (v1.11.1) and removed with the uchime algorithm [, ]. open-reference otu (operational taxonomic units) picking was performed at 97% identity using sortmerna and sumaclust and reads were clustered against the greengenes database [–]. low confidence otus were removed with a 0.1% threshold and the final otu table was normalized per sample using deseq2 []., […]

PMCID: 5769311
PMID: 29335008
DOI: 10.1186/s40168-018-0398-3

[…] filtered reads. reference otu picking was run against the greengenes [] (v13_8) database using sortmerna [] (v2.0-dev, 29/11/2014) with a minimum query coverage of 80% and de novo otu picking using sumaclust (v1.0.00; https://git.metabarcoding.org/obitools/sumaclust/wikis/home/). we filtered out otus that were called by < 0.1% of reads and then rarefied read counts to 4000 reads per sample, […]

PMCID: 5715122
PMID: 29203793
DOI: 10.1038/s41598-017-17150-2

[…] removed. the reads were subsequently dereplicated using obiuniq and a chimera removal step was performed using the uchime-denovo algorithm implemented in vsearch. the motus were delimited using the sumaclust algorithm with a constant similarity threshold of 99%. taxonomic assignment of the representative sequences for each molecular operational taxonomic unit (motu) was performed using […]


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SUMACLUST institution(s)
Department of Pediatrics, UCSD School of Medicine, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Laboratoire d'Ecologie Alpine (LECA), CNRS UMR 5553, Universite Grenoble Alpes, Grenoble, France; Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany; Department of Environmental Health, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China; Department of Informatics, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
SUMACLUST funding source(s)
Supported by HHS National Institutes of Health (NIH) under grant number 1S10OD012300, Deutsche Forschungsgemeinschaft (DFG) under grant number DU1319/1-1, the Howard Hughes Medical Institute and the Alfred P. Sloan Foundation.

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