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YARA_MAPPER(1) User Commands YARA_MAPPER(1)

NAMEΒΆ

yara_mapper - Yara Mapper

SYNOPSIS

yara_mapper [OPTIONS] <REFERENCE INDEX PREFIX> <SE-READS FILE> yara_mapper [OPTIONS] <REFERENCE INDEX PREFIX> <PE-READS FILE 1> <PE-READS FILE 2>

DESCRIPTION

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.

REQUIRED ARGUMENTS

REFERENCE_INDEX_PREFIX INPUT_PREFIX
An indexed reference genome.
READS_FILE List of INPUT_FILE's
Either one single-end or two paired-end / mate-pair read files. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

OPTIONS

-h, --help

Display the help message.

--version-check BOOL

Turn this option off to disable version update notifications of the application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.

--version

Display version information.

-v, --verbose

Displays global statistics.

-vv, --very-verbose

Displays extensive statistics for each batch of reads.
Output Options:

-o, --output-file OUTPUT_FILE

Specify an output file. Default: write the file to standard output. Valid filetypes are: .sam[.*] and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

-f, --output-format STRING

Specify an output format. Note: when specifying the option --output-file, the output format is taken from the filename extension. One of bam, sam, sam.bgzf, sam.gz, and sam.bz2. Default: sam.

-rg, --read-group STRING

Specify a read group for all records in the SAM/BAM file. Default: none.

-sa, --secondary-alignments STRING

Specify whether to output secondary alignments in the XA tag of the primary alignment, as separate secondary records, or to omit them. One of tag, record, and omit. Default: tag.

-ra, --rabema-alignments

Output alignments compatible with the Read Alignment BEnchMArk (RABEMA).
Mapping Options:

-e, --error-rate INTEGER

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. In range [0..10]. Default: 5.

-s, --strata-rate INTEGER

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. In range [0..10]. Default: 0.

-y, --sensitivity STRING

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. One of low, high, and full. Default: high.
Paired-End Mapping Options:

-ll, --library-length INTEGER

Expected library length. Default: autodetected. In range [1..inf].

-ld, --library-deviation INTEGER

Deviation from the expected library length. Default: autodetected. In range [1..inf].

-i, --indel-rate INTEGER

Rescue unaligned ends within this percentual number of indels. In range [0..50]. Default: 25.

-ni, --no-indels

Turn off the rescue of unaligned ends containing indels.
Performance Options:

-t, --threads INTEGER

Specify the number of threads to use. In range [1..2048]. Default: 4.

VERSION

Last update: yara_mapper version: 0.9.9 [tarball] SeqAn version: 2.3.1
June 2017 yara_mapper 2.3.1+dfsg-4