Fiona

Fiona is a tool for the correction of NGS read data sets. It uses a novel statistical approach for high quality and state-of-the art data structures for low resource consumptions and features a good parallelization.

You have to specify the approximate genome length of the donor in GENOME_LEN. The reads are read from the file IN.{fq,fa} and are written to OUT.fa.

Web Documentation for Fiona

Options

version-check
Turn this option off to disable version update notifications of the application.
verbose
Verbose output.
very-verbose
More verbose output.
correction-infos
Enable embedding of correction information in the output file.
global-corr-limit
Limit corrections globally and not per round.
no-final-trim-ns
Disable trimming of Ns at the end.
genome-length
Approximate length of the underlying genome.
error-rate
Approximate per-base error rate in the read set. A slight overestimation gives better results.
overlap-error-scale
The error-rate is multiplied by this scale to define the error rate cutoff in the pairwise read overlap.
from-level
Set the lower bound on the level for suffix tree DFS. Use 0 for both from-level and to-level to get automatic level detection.
to-level
Set the upper bound on the level for suffix tree DFS. Use 0 for both to-level and to-level to get automatic level detection.
depth-sample-rate
The depth sampling rate factor.
no-mask-repeats
Turn off automatic repeat masking.
kmer-repeat-ratio
The fraction of k-mers that are considered as repeats.
kmer-repeat-std-dev
Multiples of standard deviation (for k-mer repeat cut-off).
method
Selects the correction method to use.
iterations
Number of iterations. Use 0 for auto-detection.
expected
Use expected value correction with the given strictness cutoff for the expected method.
count
Use fixed count correction cutoff.
odds-ratio
Odds-ratio for the classifier method.
p-value
The p value for the expected mode. In sensitivity mode, this is the false discovery rate.
mismatches
The number of accepted mismatches per read.
overlap-sum
Filter on the number of overlapping bp needed to correct an erroneous bp. A smaller value leads to lower sensitivity, a higher value leads to higher sensitivity.
indel-length
Maximal indel length. Use 0 for correcting only substitutions and 1 for edit distance corrections on Illumina reads.
num-threads
Number of threads to use (default 1).
super-packages
Number of internal q-gram index creation runs.
packages-per-thread
Set the number of work packages per thread. More packages result lower memory consumption but possibly a longer running time.

Input Ports

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An input file with reads to be corrected. [fa,fasta,fq,fastq]

Output Ports

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An output file to store the corrected reads. [fa,fasta,fq,fastq]

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Views

Fiona Std Output
The text sent to standard out during the execution of Fiona.
Fiona Error Output
The text sent to standard error during the execution of Fiona. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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Links

Developers

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Installation

To use this node in KNIME, install the extension SeqAn from the below update site following our NodePit Product and Node Installation Guide:

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team
Plugin version: 2.4.1.202004061533
On NodePit since: 2022-12-06
Last update: 2024-12-23
KNIME versions: From v3.6 to v4.7

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