UCHIME pipeline

UCHIME specifications

Information


Unique identifier OMICS_01115
Name UCHIME
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Reference database of parent sequences provided by the use, or query ADN or ARN
Output data chimeric alignment
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 4.2
Stability Stable
Source code URL http://drive5.com/uchime/uchime4.2.40_src.tar.gz
Maintained Yes

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Publication for UCHIME

UCHIME IN pipelines

 (14)
2018
PMCID: 5834773
PMID: 29288512
DOI: 10.1111/cas.13497

[…] (shanghai, china)., operational taxonomic units were identified with a standard of at least 97% similarity in the 16s rrna sequence using usearch and chimeric sequences were identified using uchime.27, 28 classification of representative reads for each otu was carried out utilizing the rdp classifier algorithm against the silva 16s rrna database with a confidence threshold of 0.7.29, 30 […]

2018
PMCID: 5835065
PMID: 29535685
DOI: 10.3389/fmicb.2018.00280

[…] analysis. the aligned sequences were filtered using the qiime pipeline (v.1.8.0) (caporaso et al., 2010b) with the script “split_library_fastq.py.” chimera sequences were identified and removed with uchime (edgar et al., 2011) against the gold database (bernal et al., 2001). otu formation was performed following the uparse pipeline (edgar, 2013) and the dereplicated reads were clustered […]

2018
PMCID: 5911808
PMID: 29713638
DOI: 10.3389/fvets.2018.00079

[…] shallowater, tx, usa)., raw sequence data were screened, trimmed, filtered, and barcoded as well as chimera sequences depleted from the dataset using qiime v1.8.0 pipeline (31) and uchime (32). operational taxanomic units (otus) were assigned based on at least 97% sequence similarity against the greengenes reference database (33). sequence information is available […]

2017
PMCID: 5288354
PMID: 28210252
DOI: 10.3389/fmicb.2017.00143

[…] in qiime software package (quantitative insights into microbial ecology) to obtain the high-quality clean tags (caporaso et al., 2010; bokulich et al., 2013). chimera sequences were detected by uchime algorithm and were removed (edgar, 2011). then, sequences were classified to otus at 97% similarity using uparse pipeline and representative sequence for each otu was screened (edgar, 2013). […]

2017
PMCID: 5345797
PMID: 28282404
DOI: 10.1371/journal.pone.0173408

[…] reads into one single sequence. following dereplication, abundance sorting was done and singletons were discarded. otu`s were clustered at 3% divergence threshold and chimeras were eliminated using uchime [38]. representative sequences for each otu were selected and rdp classifier (16s rrna training set 14) (s1 and s2 texts) [39] was used to assign taxonomy. otu’s assigned to archaea […]

UCHIME institution(s)
Tiburon, CA, USA; Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, UK; Department of Chemistry and Biochemistry, University of Colorado, CO, USA; School of Engineering, University of Glasgow, Glasgow, UK
UCHIME funding source(s)
This package was funded by the National Institutes of Health (grant U54-HG004969), the Engineering and Physical Sciences Research Council Career Acceleration Fellowship (EP/H003851/1) and the National Institutes of Health (grants HG004872 and HHMI).

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