yara_mapper1
Yara mapper
Usage
yara_mapper [OPTIONS]
<REFERENCE
INDEX
PREFIX>
<SE-READS
FILE>
yara_mapper [OPTIONS]
<REFERENCE
INDEX
PREFIX>
<PE-READS
FILE
1>
<PE-READS
FILE
2>
Overview
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_PREFIXINPUT_PREFIX-
An indexed reference genome.
READS_FILEList 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.
Performance Options:
-
-t, --threads INTEGER -
Specify the number of threads to use. In range [1..2048]. Default: 6.
Releases
5 releases since Debian 9 (Stretch); the text changed 2 times.
--error-rate since Debian 10 (Buster);
--help since Debian 10 (Buster);
--indel-rate since Debian 10 (Buster);
--library-deviation since Debian 10 (Buster);
--library-length since Debian 10 (Buster);
--no-indels since Debian 10 (Buster);
--output-file since Debian 10 (Buster);
--output-format since Debian 10 (Buster);
--rabema-alignments since Debian 10 (Buster);
--read-group since Debian 10 (Buster);
--secondary-alignments since Debian 10 (Buster);
--sensitivity since Debian 10 (Buster);
--strata-rate since Debian 10 (Buster);
--threads since Debian 10 (Buster);
--verbose since Debian 10 (Buster);
--version since Debian 10 (Buster);
--very-verbose since Debian 10 (Buster);
-e since Debian 10 (Buster);
-f since Debian 10 (Buster);
-h since Debian 10 (Buster);
-i since Debian 10 (Buster);
-ld since Debian 10 (Buster);
-ll since Debian 10 (Buster);
-ni since Debian 10 (Buster);
-o since Debian 10 (Buster);
-ra since Debian 10 (Buster);
-rg since Debian 10 (Buster);
-s since Debian 10 (Buster);
-sa since Debian 10 (Buster);
-t since Debian 10 (Buster);
-v since Debian 10 (Buster);
-vv since Debian 10 (Buster);
-y since Debian 10 (Buster).