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FHiTINGS specifications

Information


Unique identifier OMICS_18045
Name FHiTINGS
Alternative name Fungal High-throughput Taxonomic Identification tool for use with Next-Generation Sequencing
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jordan Peccia <>

Publication for Fungal High-throughput Taxonomic Identification tool for use with Next-Generation Sequencing

FHiTINGS in pipeline

2016
PMCID: 5124938
PMID: 27892507
DOI: 10.1038/srep37929

[…] taxonomic assignments of its1 sequences were performed using blastn ver. 2.2.19 against a named fungal its sequences database, and further classified using a fungal taxonomic identification tool fhitings. the sequences were not clustered into operational taxonomic units (otus) before taxonomic assessments as clustering process may reduce the taxonomic coverage. the taxonomic identifications […]


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FHiTINGS in publications

 (5)
PMCID: 5769346
PMID: 29335027
DOI: 10.1186/s40168-017-0393-0

[…] default settings for the de novo operational taxonomic unit (otu) picking at 97% similarity for bacteria and 99% similarity for fungi. additional processing for the its sequences was performed using fhitings []. samples with fewer than 1000 16s bacterial reads (n = 16 for the lung microbiome; n = 12 for the skin microbiome) and samples with fewer than 50 its fungal reads (n = 16 for the lung […]

PMCID: 5640920
PMID: 29029638
DOI: 10.1186/s40168-017-0356-5

[…] > 97% similarity into operational taxonomic units (otus) using open reference otu picking approach for bacteria. for fungi, the data processing was similar until the chimera removal step. we used fhitings (fungal high throughput taxonomy identification in ngs) to calculate taxa-based otu groups instead of clustering []. negative and positive (bacterial and fungal mock) controls were included […]

PMCID: 5638523
PMID: 29023520
DOI: 10.1371/journal.pone.0186295

[…] for the fungal its sequences, taxonomic assignments were performed using blastn version 2.2.28+ [] against the fungalitsdatabaseid containing named fungal its sequences [] and classified using fhitings []. prior to diversity analyses, 43,769 sequences were subsampled from each library and binned into operational taxonomic units (otus) at 97% sequence identity using mothur version 1.25.0 […]

PMCID: 5124938
PMID: 27892507
DOI: 10.1038/srep37929

[…] taxonomic assignments of its1 sequences were performed using blastn ver. 2.2.19 against a named fungal its sequences database, and further classified using a fungal taxonomic identification tool fhitings. the sequences were not clustered into operational taxonomic units (otus) before taxonomic assessments as clustering process may reduce the taxonomic coverage. the taxonomic identifications […]

PMCID: 4654494
PMID: 26588216
DOI: 10.1371/journal.ppat.1005308

[…] []. operational taxonomic units (otus) were then clustered into groups of ≥97% sequence identity and chimeras were removed. taxonomic identity was assigned to the otus using blastn and the fhitings v.1-2 reference database [,]. the blastn results were input into a modified version of the fhitings program to identify the taxonomy based on blast hit frequency, e-value scores and common […]


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FHiTINGS institution(s)
Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
FHiTINGS funding source(s)
This work was supported by the Alfred P. Sloan Foundation.

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