VSEARCH protocols

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VSEARCH specifications

Information


Unique identifier OMICS_14601
Name VSEARCH
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Output format FASTA, FASTQ, SAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.3.4
Stability Stable
Requirements
libz, libbz2
Maintained Yes

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  • person_outline Torbjørn Rognes <>

Publication for VSEARCH

VSEARCH in pipelines

 (2)
2018
PMCID: 5794259
PMID: 29388911
DOI: 10.7554/eLife.31529.023

[…] hmmer and the pfam atp-cone hmm profile: pf03477 (). sequences representing the diversity of nrdb were selected by clustering all nrdb sequences from refseq at an identity threshold of 70% using vsearch (). sequences were aligned with probcons () and reliable positions for phylogenetic reconstruction were manually selected. a maximum likelihood phylogeny was estimated with fasttree 2 ()., […]

2018
PMCID: 5925865
PMID: 29755604
DOI: 10.2174/1874285801812010071

[…] crown. after the denoising, a second swarm with an aggregation equal to 3 between seeds from this first clustering was used to delineate otus. next, pcr chimeras were removed using vchime of the vsearch package []. this step was performed after clustering in order to shorten the analysis time. next, the remaining clusters were filtered. only clusters present in at least 2 samples […]


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VSEARCH in publications

 (111)
PMCID: 5952429
PMID: 29764499
DOI: 10.1186/s40168-018-0472-x

[…] the raw sequencing data was trimmed using sickle [] in paired-end mode, using default quality values and a minimum read length of 100 bp after trimming. forward and reverse read were merged using vsearch (v1.9, https://github.com/torognes/vsearch), setting minimal and maximal overlap to 280 and 350 bp, respectively. further quality control included filtering based on a maximum expected error […]

PMCID: 5935910
PMID: 29729671
DOI: 10.1186/s40168-018-0468-6

[…] spacers were removed using cutadapt v1.4.1 [], and paired reads were merged using flash v1.2.11 [] with default settings., further processing of sequence data was carried out using a combination of vsearch v2.0.3 [] and usearch v9.2.64 []. specifically, dereplication was performed with the “derep_fulllength” function in vsearch with the minimum unique group size set to 2. operational taxonomic […]

PMCID: 5931749
PMID: 29732403
DOI: 10.1126/sciadv.aap9661

[…] bp), and reads containing ambiguous bases were 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 […]

PMCID: 5938556
PMID: 29765370
DOI: 10.3389/fmicb.2018.00870

[…] uchime algorithm () from within mothur. the sequences were taxonomically classified using the default wang method to the silva 128 database and clustered into operational taxonomic units (otu) using vsearch abundance-based greedy clustering (agc; ) with a similarity threshold of 97%. singleton otus (otus occurring only once across all samples) were removed from the dataset (0.25–16.13% reads […]

PMCID: 5928015
PMID: 29713833
DOI: 10.1186/s13568-018-0600-9

[…] sequences, which were subsequently removed., the effective sequences were used in the final analysis. sequences were grouped into operational taxonomic units (otus) using the clustering program vsearch (1.9.6) against the silva 119 database that was pre-clustered at a 97% sequence identity. the rdp classifier was used to assign a taxonomic category to all the otus at a confidence threshold […]


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VSEARCH institution(s)
Department of Informatics, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Oslo, Norway; Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany; School of Engineering, University of Glasgow, Glasgow, UK; Warwick Medical School, University of Warwick, Coventry, UK; Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany; UMR LSTM, CIRAD, Montpellier, France
VSEARCH funding source(s)
This research was supported in part with computational resources at the University of Oslo provided by UNINETT Sigma2 project NN9383K and funded by the Research Council of Norway; by BBSRC CASE studentship supported by Unilever; by the MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB) project (MR/L015080/1) through fellowship (MR/M50161X/1) and by the Deutsche Forschungsgemeinschaft (grant #DU1319/1-1).

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