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Fiona specifications

Information


Unique identifier OMICS_05471
Name Fiona
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux
Programming languages C++
Parallelization OpenMP
Computer skills Advanced
Version 2.4.0
Stability Stable
Source code URL http://packages.seqan.de/fiona/
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Marcel Schulz <>
  • person_outline Hugues Richard <>

Publication for Fiona

Fiona in publications

 (4)
PMCID: 5563063
PMID: 28821237
DOI: 10.1186/s12859-017-1784-8

[…] scores. many standalone read error correction algorithms and implementations have been proposed for illumina data, including ace [], bayeshammer [], bfc [], bless [], bless 2 [], blue [], ec [], fiona [], karect [], lighter [], musket [], pollux [], quake [], quorum [], racer [], sga-ec [] and trowel []. for a comprehensive overview of the characteristics of these ec tools […]

PMCID: 5361737
PMID: 28262558
DOI: 10.1016/j.chembiol.2017.02.006

[…] were constructed using the nebnext ultra dna kit (neb) and sequenced on a nextseq500 (illumina) with 83 bp reads in both directions. one hundred million pairs of reads were error corrected using fiona () prior to de novo genome assembly using spades (). this process was repeated using a separate 100 million pair read, and a consensus assembly between the two de novo assemblies was created […]

PMCID: 4848821
PMID: 27127540
DOI: 10.1186/s13040-016-0095-3

[…] and distributed environments. the number of tools for ngs that have been released using seqan is remarkable and proves how such open programming approach is advantageous [–]. bowtie, lambda and fiona are written in seqan, the latter of which is one of the fastest local aligners for ngs data and error correction tool, and it may become an alternative to blast. another toolset similar […]

PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] optimize correction (section ‘optimal k-mer length’ and supplementary note s3). an optimization idea—first introduced for suffix trees []—was recently implemented for suffix arrays in psaec [] and fiona []: they construct only a partial suffix array up to a specified order h, in a process they parallelize. this effectively means that suffixes are only sorted according to their first h bases, […]


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Fiona institution(s)
Multimodal Computing and Interaction, Saarland University and Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, Saarland, Germany; Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany; Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France; CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France
Fiona funding source(s)
Supported by the IMPRS-CBSC Berlin, the BMBF [16V0080] and partly by a JSPS [PE11014] fellowship.

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