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Protocols

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


No version available

Documentation


Maintainers


  • person_outline Jenya Kopylov
  • person_outline Celine Mercier

Publication for SUMACLUST

SUMACLUST citations

 (28)
library_books

Environmental DNA illuminates the dark diversity of sharks

2018
Sci Adv
PMCID: 5931749
PMID: 29732403
DOI: 10.1126/sciadv.aap9661

[…] re 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 e […]

call_split

Use of dietary indices to control for diet in human gut microbiota studies

2018
Microbiome
PMCID: 5918560
PMID: 29695307
DOI: 10.1186/s40168-018-0455-y
call_split See protocol

[…] essed 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 to rem […]

library_books

The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster

2018
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 []. […]

library_books

Multi omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

2018
Microbiome
PMCID: 5769311
PMID: 29335008
DOI: 10.1186/s40168-018-0398-3

[…] e 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, whic […]

library_books

Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact

2017
Sci Rep
PMCID: 5715122
PMID: 29203793
DOI: 10.1038/s41598-017-17150-2

[…] o 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 the ecota […]

library_books

Detection of subclonal L1 transductions in colorectal cancer by long distance inverse PCR and Nanopore sequencing

2017
Sci Rep
PMCID: 5673974
PMID: 29109480
DOI: 10.1038/s41598-017-15076-3

[…] m the candidate insertions were processed with ampCorrect, a Nanopore read correction method similar to nanocorrect, to obtain accurate consensus sequences for the amplicons. Briefly, ampCorrect uses sumaclust (http://metabarcoding.org/sumatra) to cluster the reads, requiring 60% sequence similarity and poaV2 -do global to align multiple reads. The consensus sequence is treated as corrected sequen […]

Citations

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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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