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 1.0~beta.18                    December 2017                            SNAP-ALIGNER_INDEX(1)