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UCHIME specifications


Unique identifier OMICS_01115
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




No version available


Publication for UCHIME

UCHIME citations


Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks

Sci Rep
PMCID: 5943461
PMID: 29743727
DOI: 10.1038/s41598-018-25760-7

[…] f the raw tags was performed under specific filtering conditions according to the QIIME to obtain the high-quality clean tags. The tags were compared with the reference database (Gold Database) using UCHIME algorithm to detect chimera sequences, which were removed. The resulted effective tags were analyzed with Uparse software (V8.1.1861). Sequences with ≥97% similarity were assigned to the same o […]


Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild Type Salmonella enterica Serovar Typhi

PMCID: 5941076
PMID: 29739901
DOI: 10.1128/mBio.00686-18

[…] nsecutive low-quality bases, (ii) no reads with ambiguous base calls were used, and (iii) reads with <150 bp after trimming were discarded. Demultiplexing was performed with QIIME (version 1.8.0) (). UCHIME v5.1 was conducted for de novo chimera detection and removal. Sequences were clustered as operational taxonomic units (OTUs) based on a 97% cutoff with USEARCH. Taxonomic ranks were assigned to […]


Microbial community analysis and biodeterioration of waterlogged archaeological wood from the Nanhai No. 1 shipwreck during storage

Sci Rep
PMCID: 5940862
PMID: 29740020
DOI: 10.1038/s41598-018-25484-8

[…] ding to the QIIME (v. 1.7.0) quality control protocol. Fungal tags were compared with the Unite database (v. 20140703), bacterial tags were compared to the SILVA Gold database (v. 20110519) using the UCHIME algorithm (v. 4.1) to detect chimaera sequences, and sequences flagged as chimaeras were then removed. The resultant high-quality sequences were used for further analyses. OTU clustering analys […]


Networks of genetic similarity reveal non neutral processes shape strain structure in Plasmodium falciparum

Nat Commun
PMCID: 5940794
PMID: 29739937
DOI: 10.1038/s41467-018-04219-3
call_split See protocol

[…] ed between a read pair was set to 20nt. Low-quality reads were filtered if they had more than one expected error using the fastq_filter option of Usearch v8.1.1832. Next, chimeras were filtered using Uchime denovo and then the filtered reads were clustered using the cluster_fast function of Usearch after the removal of singletons to reduce the impact of errors. A threshold of 96% identity was used […]


The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses

PMCID: 5936483
PMID: 29730829
DOI: 10.1186/s13568-018-0607-2
call_split See protocol

[…] imer sequence and minimum average quality score of 20 over a window of 50 base pairs. Improved reads were aligned to the Silva nr database (release v123) (Quast et al. ). Chimera’s were removed using Uchime. Next, reads were classified at bootstrap value of 80%, after which the unwanted and non-target lineages Archaea, Eukaryota, chloroplast, mitochondria and unknown were removed. The final datase […]


Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging

Front Microbiol
PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862
call_split See protocol

[…] ckage Cutadapt v1.14 was used to remove forward and reverse sequencing primers from the merged reads of each dataset. The resulting sequence tags were compared to the Gold database (http://drive5.com/uchime/gold.fa) to remove chimera sequences using the USEARCH package (http://www.drive5.com/uparse/) (Edgar, ). Only sequence tags with length >400 bp were retained for subsequent analysis. The opera […]


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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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