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.