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

gmap_build 2017-11-15-1                           December 2017                                    GMAP_BUILD(1)