NAME

       snap-aligner_index - scalable nucleotide alignment program

SYNOPSIS

       snap-aligner index <input.fa> <output-dir> [<options>]

DESCRIPTION

       Welcome to SNAP version 1.0.0.

OPTIONS

       -s     Seed size (default: 27)

       -h     Hash table slack (default: 0.3)

       -t     Specify  the  maximum  number of threads to use. Default is the number of cores. Do
              not leave a space after the -t, e.g., -t16

       -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 and tab characters are terminators  for  chromosome  names
              (see -B above).  This may be used in addition to other terminators specified by -B.
              -B and -bSpace are case sensitive.

       -p     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.
              Specify the amount of padding directly after -p without a space.

       -H     Build  a histogram of seed popularity.  This is just for information, it's not used
              by SNAP.  Specify the histogram file name  directly  after  -H  without  leaving  a
              space.

       -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.  By default it's autoselected based on
              the seed size.

       -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 20 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 based on  seed  size:  4  if
              it's 20 or greater, 5 otherwise.

       -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.

       -AutoAlt-
              Don't  automatically  mark  ALT  contigs.  Otherwise, any contig whose name ends in
              '_alt' (regardless of captialization) or starts  with  HLA-  will  be  marked  ALT.
              Others will not.

       -maxAltContigSize  Specify  a  size at or below which all contigs are automatically marked
              ALT, unless overridden by name using the args below

       -altContigName
              Specify the (case independent) name of an alt to mark a  contig.   You  can  supply
              this parameter as often as you'd like

       -altContigFile
              Specify  the name of a file with a list of alt contig names, one per line.  You may
              specify this as often as you'd like

       -nonAltContigName Specify the name of a contig that's not an alt, regardless of its size

       -nonAltContigFile Specify the name of a file that contains a  list  of  contigs  (one  per
              line) that will not be marked ALT regardless of size