ChimeraSlayer pipeline

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

 (13)
2018
PMCID: 5896095
PMID: 29642886
DOI: 10.1186/s12870-018-1272-y

[…] [29] of qiime [30] with minor modifications which are described in detail in schneijderberg et al. (in preparation). in short, reads were quality filtered and filtered for chimeras using chimeraslayer. using a 97% identity threshold, de novo otus were determined, which were taxonomically assigned using the rdp classifier with the greengenes database. otus related to mitochondrial […]

2017
PMCID: 5313486
PMID: 28261182
DOI: 10.3389/fmicb.2017.00226

[…] 2010). taxonomy was assigned to each otu using the ribosomal database project (rdp) classifier with a minimum confidence threshold of 80% (wang et al., 2007). the chimeric sequences were removed by chimeraslayer (haas et al., 2011) and the final otu table was filtered based on the criteria that the otu had to be observed in the three replicates to be retained and that one otu had to contain 57 […]

2017
PMCID: 5317032
PMID: 28218290
DOI: 10.1038/srep42625

[…] length of 350 bp and less than 2 or more undetermined nucleotides. the filtered dataset, containing only high quality sequences, was submitted to a conservative chimera detection filter using the chimeraslayer method60. selected high quality chimera–free sequences were clustered into operational taxonomic units (otus) within reads using the uclust61 with a pairwise identity threshold […]

2017
PMCID: 5452829
PMID: 28389534
DOI: 10.1128/AEM.03430-16

[…] pynast software (63). taxonomy was assigned to each otu using the ribosomal database project (rdp) classifier with a minimum confidence threshold of 80% (64). the chimeric sequences were removed by chimeraslayer (65), and the final otu table was filtered based on the criterion that otus observed in all three replicates were retained. the otu tables were subsampled (according to the sample […]

2016
PMCID: 4829023
PMID: 27148171
DOI: 10.3389/fmicb.2016.00460

[…] sequence identity using uclust (edgar, 2010) and taxonomy was assigned against the greengenes database (version 13/8/2013) using blast (altschul et al., 1990). chimeric sequences were detected using chimeraslayer (haas et al., 2011) and filtered from the dataset. sequences were then rarefied to the same depth to remove the effect of sampling effort upon analysis., seasonal differences […]

ChimeraSlayer institution(s)
Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA, USA

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