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Bisar

This program reads three-letter mappings of bisulfite reads and computes local pairwise four-letter realignments using an advanced statistical alignment model.

Web Documentation for Bisar

Options

version-check: Turn this option off to disable version update notifications of the application.
max3-error: Max. error rate in 3-letter alphabet.
max4-error: Max. error rate in 4-letter alphabet.
min-mapq: Min required mapping quality.
ns-subst-errors: Use empirical substitution error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Dohm et al. 2008).
ns-ins-errors: Use empirical insertion error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Minoche et al. 2011).
ns-del-errors: Use empirical deletion error frequencies of Illumina sequencing data for alignment scoring scheme (corresponding to Minoche et al. 2011).
del-error-rate: Deletion error rate.
gap-open-score: Gap open score (original, must be proportional to mismatch scores).
gap-extend-score: Gap extend score.
bs-conversion-rate: Bisulfite conversion rate.
global-meth-rate: Global methylation rate.
seq-identity: Sequence identity used for substitution matrix.
ref-n: Rate of Ns in reference sequence.
quiet: Set verbosity to a minimum.
verbose: Enable verbose output.
very-verbose: Enable very verbose output.

Input Ports

: SAM input file containing three-letter read alignments (must be sorted by query names). [bam,sam,sam.bgzf,sam.gz]
: A reference 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]
: Either one (single-end) or two (paired-end) read files. [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]

Output Ports

: Mapping output file. [bam,sam,sam.bgzf,sam.gz]

Popular Predecessors

Popular Successors

Views

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

Workflows

BS-Seq Analysis WorkflowSeqAn

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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