ChimeraSlayer protocols

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ChimeraSlayer specifications

Information


Unique identifier OMICS_01113
Name ChimeraSlayer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for ChimeraSlayer

ChimeraSlayer in pipelines

 (70)
2018
PMCID: 5762819
PMID: 29321642
DOI: 10.1038/s41598-017-18348-0

[…] sequences. the unique sequence set was classified into otus under 98.6% threshold identity using uclust. the potential chimerical sequences in the representative set of otus were removed by chimeraslayer. subsequently, the taxonomy of each otu representative sequence was assigned using the ribosomal database project ii database classified at a minimum bootstrap threshold of 80%. […]

2018
PMCID: 5789842
PMID: 29382896
DOI: 10.1038/s41598-018-20302-7

[…] analysed by the qiime pipeline, aligning them against the silva database (v119) by means of the pynast aligner using the open-reference strategy and clustering them at 97% of identity. the chimeraslayer tool was used to assess the presence of chimeric sequences, which were not found in any sample., all bioinformatic analyses were performed using the same number of sequences to properly […]

2018
PMCID: 5829075
PMID: 29487373
DOI: 10.1038/s41598-018-21892-y

[…] error = 0, minimum length = 200 bp) using the quantitative insights into microbial ecology (qiime) pipeline v 1.9.0., chimeric sequences were identified using the usearch algorithm against the chimeraslayer reference database (identify_chimeric_seqs.py; version ‘microbiomeutil-r20110519’) and subsequently removed from the dataset (filter_fasta.py) prior to sequence alignment. sequences […]

2018
PMCID: 5835077
PMID: 29535686
DOI: 10.3389/fmicb.2018.00295

[…] rrna gene reads were classified into operational taxonomic units (otus) with uclust method at 97% similarity (caporaso et al., ; kuczynski et al., ). then the chimeric sequences were identified with chimeraslayer program. after removing of chimeric sequences, all the 16s rrna gene reads and a representative sequence of each otu were used for the rdp-based phylum level classification, […]

2018
PMCID: 5891625
PMID: 29666616
DOI: 10.3389/fmicb.2018.00629

[…] the sequence analysis was conducted using the qiime 1.9.0 package (rrid:scr_008249) (). paired-end reads were assembled using seqprep (rrid:scr_013004). chimeric sequences were identified with chimeraslayer (rrid:scr_013283) () and verified manually before removal from the data set. if a putative chimera was present in at least two independent samples, the sequences were retained […]


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ChimeraSlayer in publications

 (355)
PMCID: 5946492
PMID: 29774049
DOI: 10.1186/s13068-018-1136-6

[…] [] by running the program against reference database silva ssu 119 [] clustered at 97% identity for 80 iterations. reconstructed 16s rrna gene sequences (> 1200 bp) post-chimera checking using chimeraslayer were annotated by blastn search against both silva ssu 115 and greengenes (2013–5 release) databases at an e value of 1e−20. the relative abundance of each 16s rrna gene sequences […]

PMCID: 5938409
PMID: 29765368
DOI: 10.3389/fmicb.2018.00860

[…] analysis (). briefly, 16s rrna operational taxonomic units (otus) were clustered using an open-reference otu picking protocol based on 97% nucleotide similarity with the uclust algorithm (), and chimeraslayer was applied to remove chimeric sequences (). the relative abundance of each otu was determined as a proportion of the sum of sequences for every sample, taxonomic relative abundance […]

PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] was globally trimmed to 591 bp, representing the longest coding region common to most sequences, and shorter sequences were excluded., screening for chimeric sequences was performed with uchime, chimeraslayer and by intensively inspecting phylogenetic trees and sequence alignments. chimera screening with uchime and chimeraslayer was based on a newly assembled reference database, since […]

PMCID: 5930336
PMID: 29475863
DOI: 10.1128/AEM.02156-17

[…] and or homopolymers of >8 bp. singletons were removed, operational taxonomic units (otus) were clustered at 97% nucleotide sequence similarity, and a chimera check was performed against the gold chimeraslayer reference database using usearch (). sequences were subsampled to 7,145 sequences per sample., vibrio species otus with >100 sequences in the rarefied data set were aligned […]

PMCID: 5892011
PMID: 29631623
DOI: 10.1186/s40168-018-0446-z

[…] generate ribosomal sequence variants (rsvs). these were exported and further chimera filtered using both the de novo and reference-based chimera filtering implemented in usearch v8.1.1861 with the chimeraslayer gold database v20110519 []. the remaining rsvs were classified with mothur v1.38 [] against the rdp database version 11.4, as well as classified with spingo to species level []. […]


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ChimeraSlayer institution(s)
Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA, USA
ChimeraSlayer funding source(s)
Supported by NIH with awards to the Baylor College of Medicine (grants U54-HG003273 and U54-HG004973), the Broad Institute (grant U54-HG004969 and NIAID contract HHSN27220090018C), the J. Craig Venter Institute (NIAID contract N01-AI30071 and grant U54-AI084844), Washington University (grants U54-HG003079 and U54-HG004968), and NIH common fund contract U01-HG004866, a Data Analysis and Coordination Center for the Human Microbiome Project.

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