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ITSx specifications

Information


Unique identifier OMICS_25040
Name ITSx
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1b
Stability Beta
Maintained Yes

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https://anaconda.org/bioconda/itsx

Publication for ITSx

ITSx in pipelines

 (11)
2018
PMCID: 5874253
PMID: 29593263
DOI: 10.1038/s41426-018-0049-6

[…] demultiplexed data was screened for chimeras with vsearch using the usearch_ref option against the unite-based fungal chimera dataset, and subsequently screened for fungal its2 sequences with itsx. sequences were dereplicated on the first 100 bases with the prefix_suffix otu picker in qiime. otus were defined de novo with swarm at a resolution of 1, and taxonomy was assigned using blast […]

2017
PMCID: 5306204
PMID: 28261162
DOI: 10.3389/fmicb.2017.00180

[…] we compared three commonly used analysis pipelines mothur, qiime, and micca, employing an in silico created fungal its1 mock community. therefore, 582,779 its1 fragments were extracted by itsx (bengtsson-palme et al., ) from the public unite sequence collection (version 7, comprising 656,899 sequences). amplicons were filtered for ambiguous lineage definitions, resulting in 345,201 […]

2017
PMCID: 5383709
PMID: 28439263
DOI: 10.3389/fmicb.2017.00591

[…] of tag barcodes and identified sequences using the seed platform (overbeek et al., ). the barcode sequences were removed using seed. the its1 region was then detected and extracted with the itsx (an improved software), as the itsx tool has the capacity to extract higher proportions of true positives and remove non-its sequences from data sets (bengtsson-palme et al., ). the obtained […]

2017
PMCID: 5516253
PMID: 28720730
DOI: 10.1128/mBio.00764-17

[…] sequence length of 10, and a quality trim score of 10. reads were then assembled into single sequences with pandaseq (), and the flanking ribosomal small subunit and 5.8s regions were removed with itsx (). chimeric sequences were detected and discarded with usearch61 (). otu clustering at 97% identity was performed with the qiime () implementation of uclust (), using an open reference strategy […]

2017
PMCID: 5575336
PMID: 28851897
DOI: 10.1038/s41598-017-08554-1

[…] 576,133 bacterial and 806,387 fungal sequences after joining and quality trimming. before picking the operational taxonomic units (otu), the fungal its1 region was extracted from reads using itsx algorithm. both 16s and its1 amplicons were trimmed to equal lengths in order to avoid spurious otu clusters. bacterial reads were clustered (more than 97% similarity) to otus using […]


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ITSx in publications

 (41)
PMCID: 5874253
PMID: 29593263
DOI: 10.1038/s41426-018-0049-6

[…] demultiplexed data was screened for chimeras with vsearch using the usearch_ref option against the unite-based fungal chimera dataset, and subsequently screened for fungal its2 sequences with itsx. sequences were dereplicated on the first 100 bases with the prefix_suffix otu picker in qiime. otus were defined de novo with swarm at a resolution of 1, and taxonomy was assigned using blast […]

PMCID: 5860773
PMID: 29558527
DOI: 10.1371/journal.pone.0194489

[…] the filtering (minimum length 150 bp, minimum average quality score 20, maximum length of homopolymer 8, maximum number of primer mismatches 3) were discarded. the its2 region was extracted with itsx v1.0.11 [] by selecting the fungal (f) profile option. chimeric reads were identified and filtered out with uchime v4.0 algorithm using the reference dataset updated on 01.12.2016 [, ] to obtain […]

PMCID: 5845876
PMID: 29563897
DOI: 10.3389/fmicb.2018.00294

[…] was made with snakemake () as available at doi: https://doi.org/10.5281/zenodo.597131 (). this pipeline was also used for its with the following adjustments: (1) its2 regions where extracted using itsx 1.0.11 (). (2) using the unite database () provided by rdp the sequences were classified. otus without affiliation to at least kingdom level were excluded from the downstream beta-diversity […]

PMCID: 5791994
PMID: 29385188
DOI: 10.1371/journal.pone.0191913

[…] with the uchime algorithm (version 4.2.4) []. otu picking was performed at 97% sequence similarity with uclust (version 2.1). fungal its1 and its2 reads were extracted from its sequences with itsx 1.0.11 []. the its1 and its2 sequences were compared with a blast search against the unite fungal its database (https://unite.ut.ee/). we parsed the blast outputs in megan 6 [] for initial […]

PMCID: 5711903
PMID: 29196717
DOI: 10.1038/s41598-017-17132-4

[…] algorithm uclust 2.1, implemented in usearch v.6.0.203. de novo chimera detection was performed with the uchime algorithm. otu picking was performed at 97% sequence similarity with uclust 2.1. itsx 1.0.11 was used to extract fungal its1 and its2 reads from its sequences. the its1 and its2 sequences were compared using blast search against the unite fungal its database […]


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ITSx institution(s)
Department of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Goteborg, Sweden; Department of Organismal Biology, Uppsala University, Uppsala, Sweden; Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland; Molecular Ecology, Agroscope Reckenholz-Tanikon Research Station ART, Zurich, Switzerland; Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Department of Biological and Environmental Sciences, University of Gothenburg, Goteborg, Sweden; Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA; Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany; Botany Department, University of Hawai‘i at Manoa, Honolulu, HI, USA; Division of Biology, Kansas State University, Manhattan, KS, USA; Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany; Department of Mathematical Statistics, Chalmers University of Technology, Goteborg, Sweden; Natural History Museum, University of Tartu, Tartu, Estonia; Department of Shipping and Marine Technology, Chalmers University of Technology, Goteborg, Sweden; Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
ITSx funding source(s)
Supported by the FORMAS (grant FORMAS, 215-2011-498) and the Carl Stenholm Foundation.

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