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YaraMapper

Generic Workflow Nodes for KNIME: SeqAn version 2.4.1.202004061533 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Yara - Yet Another Read Aligner.

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

(c) Copyright 2011-2014 by Enrico Siragusa.

(c) Copyright 2013 by NVIDIA Corporation.

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

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An indexed reference genome. [*]
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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

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

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install SeqAn from the following update site:

KNIME 4.2

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

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Developers

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