snap-aligner-index(1)
NAME
snap-aligner_index - scalable nucleotide alignment program
SYNOPSIS
snap-aligner index <input.fa> <output-dir> [<options>]
DESCRIPTION
Welcome to SNAP version 1.0beta.18.
OPTIONS
-s Seed size (default: 20)
-h Hash table slack (default: 0.3)
-hg19 Use pre-computed table bias for hg19, which results in better
speed, balance, and a smaller index, but only works for the
complete human reference.
-Ofactor
This parameter is deprecated and will be ignored.
-tMaxThreads
Specify the maximum number of threads to use. Default is the
number of cores.
-B<chars>
Specify characters to use as chromosome name terminators in the
FASTA header line; these characters and anything after are not
part of the chromosome name. You must specify all characters on
a single -B switch. So, for example, with -B_|, the FASTA
header line '>chr1|Chromosome 1' would generate a chromosome
named 'chr1'. There's a separate flag for indicating that a
space is a terminator.
-bSpace
Indicates that the space character is a terminator for
chromosome names (see -B above). This may be used in addition
to other terminators specified by -B. -B and -bSpace are case
sensitive.
-pPadding
Specify the number of Ns to put as padding between chromosomes.
This must be as large as the largest edit distance you'll ever
use, and there's a performance advantage to have it be bigger
than any read you'll process. Default is 500
-HHistogramFile
Build a histogram of seed popularity. This is just for
information, it's not used by SNAP.
-exact Compute hash table sizes exactly. This will slow down index
build, but usually will result in smaller indices.
-keysize
The number of bytes to use for the hash table key. Larger
values increase SNAP's memory footprint, but allow larger seeds.
Default: 4
-large Build a larger index that's a little faster, particualrly for
runs with quick/inaccurate parameters. Increases index size by
about 30%, depending on the other index parameters and the
contents of the reference genome
-locationSize
The size of the genome locations stored in the index. This can
be from 4 to 8 bytes. The locations need to be big enough not
only to index the genome, but also to allow some space for
representing seeds that occur multiple times. For the human
genome, it will fit with four byte locations if the seed size is
19 or larger, but needs 5 (or more) for smaller seeds. Making
the location size bigger than necessary will just waste (lots
of) space, so unless you're doing something quite unusual, the
right answer is 4 or 5. Default is 4
-sm Use a temp file to work better in smaller memory. This only
helps a little, but can be the difference if you're close. In
particular, this will generally use less memory than the index
will use once it's built, so if this doesn't work you won't be
able to use the index anyway. However, if you've got sufficient
memory to begin with, this option will just slow down the index
build by doing extra, useless IO.
snap-aligner_index 0.18~1.0~beta.1August12016 SNAP-ALIGNER_INDEX(1)
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