NAME

       snap-aligner_index - scalable nucleotide alignment program

SYNOPSIS

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

DESCRIPTION

       Welcome to SNAP version 2.0.3.

OPTIONS

       -s     Seed size (default: 24)

       -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.  This is the default.

       -bSpace-
              Indicates that space and tab characters should be included in chromosome names.

       -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  or  gap between paired-end reads.  Default is 2000.  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,  particularly  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

       -altLiftoverFile
              Specify the file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit

       -q     Quiet  mode: don't print status messages (other than the welcome message which is printed prior to
              parsing args).  Error messages are still printed.

       -qq    Super quiet mode: don't print status or error messages

snap-aligner index 2.0.3                          January 2024                             SNAP-ALIGNER_INDEX(1)