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YaraMapper

Yara - Yet Another Read Aligner.

See http://www.seqan.de/projects/yara for more information.

Web Documentation for YaraMapper

Options

version-check: Turn this option off to disable version update notifications of the application.
verbose: Displays global statistics.
very-verbose: Displays extensive statistics for each batch of reads.
output-format: Specify an output format. Note: when specifying the option --output-file, the output format is taken from the filename extension.
read-group: Specify a read group for all records in the SAM/BAM file.
secondary-matches: Specify whether to output secondary matches in the XA tag of the primary alignment, as separate secondary records, or to omit them.
align-secondary: Compute and output co- and suboptimal match alignments. Ignored if '-sa omit' is set.
rabema-alignments: Output alignments compatible with the Read Alignment BEnchMArk (RABEMA).
error-rate: Consider alignments within this percentual number of errors. Increase this threshold to increase the number of mapped reads. Decrease this threshold to decrease the runtime.
strata-rate: Consider suboptimal alignments within this percentual number of errors from the optimal alignment. Increase this threshold to increase the number of alternative alignments at the expense of runtime.
strata-count: Consider suboptimal alignments within this absolute number of errors from the optimal alignment. Increase this threshold to increase the number of alternative alignments at the expense of runtime.
sensitivity: Sensitivity with respect to edit distance. Full sensitivity guarantees to find all considered alignments but increases runtime, low sensitivity decreases runtime by breaking such guarantee.
library-length: Expected library length. Default: autodetected.
library-deviation: Deviation from the expected library length. Default: autodetected.
indel-rate: Rescue unaligned ends within this percentual number of indels.
no-indels: Turn off the rescue of unaligned ends containing indels.
threads: Specify the number of threads to use.

Input Ports

: An indexed reference genome. [*]
: Either one single-end or two paired-end / mate-pair read files. [fq,fq.bgzf,fq.gz,fq.bz2,fastq,fastq.bgzf,fastq.gz,fastq.bz2,fa,fa.bgzf,fa.gz,fa.bz2,fasta,fasta.bgzf,fasta.gz,fasta.bz2,faa,faa.bgzf,faa.gz,faa.bz2,ffn,ffn.bgzf,ffn.gz,ffn.bz2,fna,fna.bgzf,fna.gz,fna.bz2,frn,frn.bgzf,frn.gz,frn.bz2,embl,embl.bgzf,embl.gz,embl.bz2,gbk,gbk.bgzf,gbk.gz,gbk.bz2,raw,raw.bgzf,raw.gz,raw.bz2,sam,sam.bgzf,sam.gz,sam.bz2,bam]

Output Ports

: Specify an output file. Default: write the file to standard output. [bam,sam,sam.bgzf,sam.gz,sam.bz2]

Popular Predecessors

Popular Successors

Views

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

Workflows

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: 2026-01-01

KNIME versions: From v3.6 to v4.7

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