NAME¶
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
- 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.
- -t, --threads INTEGER
- Specify the number of threads to use. In range [1..2048]. Default:
4.
