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.