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