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ComputeGain

This program computes the read correction tool metric GAIN. It takes a genome FASTA file and two SAM file with read alignments before and after correction. It then computes various statistics and computes the GAIN, based on the edit or Hamming distance for reach read before and after correction.

Web Documentation for ComputeGain

Options

version-check: Turn this option off to disable version update notifications of the application.
quiet: Disable most output.
verbose: Enable more verbose output.
very-verbose: Enable even more verbose output.
num-threads: Number of threads to use.
chunk-size: Chunk size.
max-chunks: Maximal number of chunks to read (0=disabled).
padding: Additional genome characters to use for alignment in percent of the origina read length.
metric: The metric type to use.
min-unclipped-bases: Reads with fewer unclipped bases are ignored. Set to 0 to disable ignoring because of this.
max-error-rate: Reads with a higher error rate in the initial mapping are ignored. Given in percent. Set to 0 to disable ignoring because of this.
max-error-count: Reads with a higher error count in the initial mapping are ignored. Given in percent. Set to -1 to disable ignoring because of this.
log-all: Log all not only introduced/removed errors.
no-check-sorting: No checking for reads being sorted.

Input Ports

: Genome file. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
: Pre-correction SAM file. [sam,bam]
: Post-correction SAM file. [sam,opt.]
: Post-correction FASTQ or FASTA file. [fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz,opt.]

Output Ports

: Write log about introduced/removed errors to this file. []

Popular Predecessors

Dfi100 %

Popular Successors

ZipLoopEnd100 %

Views

ComputeGain Std Output: The text sent to standard out during the execution of ComputeGain.
ComputeGain Error Output: The text sent to standard error during the execution of ComputeGain. (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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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: 2025-06-26

KNIME versions: From v3.6 to v4.7

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