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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

 (204)
2018
PMCID: 5784121
PMID: 29367671
DOI: 10.1038/s41598-018-19912-y

[…] between the barcode and primer were processed further. the sequences were trimmed to 200 bp before clustering with uparse at a 97% similarity level. chimeras in the sequences were filtered with uchime. the sequences analysis was performed using the usearch package. representative sequences were classified on rdp pipeline (http://pyro.cme.msu.edu/). an otu table was rarefied to 2891 and 540 […]

2018
PMCID: 5787670
PMID: 29416529
DOI: 10.3389/fmicb.2018.00031

[…] and –max-overlap which were set to 140 and 230, respectively. successfully combined reads were filtered based on quality using seqtk trimfq with default parameters. chimeras were removed with the uchime2_ref algorithm of usearch (version 9.2.64) (). the taxonomy of reads was assigned using rdp classifier 2.12 () to generate phylum to genus level composition matrices. bootstrap values […]

2018
PMCID: 5792618
PMID: 29435244
DOI: 10.1002/ece3.3746

[…] filtering the raw tags using the quality controlled process of qiime (version 1.7.0; caporaso et al., ). to determine chimera sequences, the clean tags were aligned by the method that compares the uchime algorithm to the gold database (http://drive5.com/uchime/uchime_download.html), in order to find out chimera sequences. finally, the chimera sequences were removed to develop the effective […]

2018
PMCID: 5792648
PMID: 29386622
DOI: 10.1038/s41598-018-20414-0

[…] conversion of reads from fastq to fasta format was performed with qiime (1.9.0 + dfsg-0biolinux5) “convert_fastaqual_fastq.py”. chimera sequences were removed using usearch (7.0.1090_i86linux32) (-uchime option) and greengenes as reference database. taxonomic assignment was performed using bayesian rdp classifier trained with rdp (v11), greengenes (13 08), or silva (v128). output of rdp […]

2018
PMCID: 5797343
PMID: 29394957
DOI: 10.1186/s40168-018-0412-9

[…] were provided with taxonomic information using the “assign_taxonomy.py” command in qiime [] based on the greengenes reference database (may 2013 version, 99,322 sequences). chimeras were detected in uchime2 (high-confidence mode) against the greengenes database to minimize risk of identifying false-positive chimera otus []. otu lineages present in an average of > 5% of reads in negative […]

UCHIME in publications

 (1527)
PMCID: 5943461
PMID: 29743727
DOI: 10.1038/s41598-018-25760-7

[…] 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 […]

PMCID: 5940794
PMID: 29739937
DOI: 10.1038/s41467-018-04219-3

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862

[…] 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. […]

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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