NAME

       gmap_build - Tool for genome database creation for GMAP or GSNAP

SYNOPSIS

       gmap_build [options...] -d <genomename> <fasta_files>

DESCRIPTION

       gmap_build: Builds a gmap database for a genome to be used by GMAP or GSNAP.  Part of GMAP
       package, version 2017-11-15.

       A simplified alternative to using the program gmap_setup, which creates a Makefile.

OPTIONS

       -D, --dir=STRING
              Destination directory for installation (defaults to gmapdb directory  specified  at
              configure time)

       -d, --db=STRING
              Genome name

       -n, --names=STRING
              Substitute  names  for  chromosomes,  provided in a file.  The file should have one
              line for each chromosome name to be changed, with the original FASTA name in column
              1 and the desired chromosome name in column 2.  This provides an easy way to change
              the names of chromosomes, for example, to add or remove the "chr" prefix.  Column 2
              may  be blank, which indicates no name change.  This file can also be combined with
              --sort=names to provide a particular order for the chromosomes in the genome index.

       -M, --mdflag=STRING
              Use MD file from NCBI for mapping contigs to chromosomal coordinates

       -C, --contigs-are-mapped
              Find a chromosomal region in each FASTA header line.  Useful for contigs that  have
              been mapped to chromosomal coordinates.  Ignored if the --mdflag is provided.

       -z, --compression=STRING
              Use given compression types (separated by commas; default is bitpack64) bitpack64 -
              optimized for modern computers with SIMD instructions (recommended)  all  -  create
              all  available compression types, currently bitpack64 none - do not compress offset
              files (I believe this is no longer supported)

       -k, --kmer=INT
              k-mer value for genomic index (allowed: 15 or less, default is 15)

       -q INT sampling interval for genomoe (allowed: 1-3, default 3)

       -s, --sort=STRING
              Sort chromosomes using given method: none -  use  chromosomes  as  found  in  FASTA
              file(s)  alpha - sort chromosomes alphabetically (chr10 before chr 1) numeric-alpha
              - chr1, chr1U, chr2, chrM, chrU, chrX, chrY chrom - chr1, chr2, chrM,  chrX,  chrY,
              chr1U, chrU names - sort chromosomes based on file provided to --names flag

       -g, --gunzip
              Files are gzipped, so need to gunzip each file first

       -E, --fasta-pipe=STRING
              Interpret argument as a command, instead of a list of FASTA files

       -w INT Wait (sleep) this many seconds after each step (default 2)

       -c, --circular=STRING
              Circular  chromosomes  (either  a  list  of  chromosomes separated by a comma, or a
              filename containing circular chromosomes, one per line).  If you  use  the  --names
              feature,  then  you  should  use  the  original  name  of  the  chromosome, not the
              substitute name, for this option.

       -2, --altscaffold=STRING
              File  with  alt  scaffold  info,  listing  alternate  scaffolds,  one   per   line,
              tab-delimited,  with  the  following fields: (1) alt_scaf_acc, (2) parent_name, (3)
              orientation,  (4)  alt_scaf_start,  (5)  alt_scaf_stop,   (6)   parent_start,   (7)
              parent_end.

       -e, --nmessages=INT
              Maximum number of messages (warnings, contig reports) to report (default 50)

       --build-sarray=INT
              Whether to build suffix array: 0=no, 1=yes (default)

   Obsolete options:
       -T STRING
              Temporary  build  directory  (may  need  to specify if you run out of space in your
              current directory) This  is  no  longer  necessary,  since  gmap_build  now  builds
              directly in the destination (or -D) directory.

       Other tools of GMAP suite are located in /usr/lib/gmap