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 2020-04-08.

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 contigs, provided in a file.  The file have two formats:

       1.     A  file  with one column per line, with each line corresponding to a FASTA file, in
              the order given to gmap_build.  The chromosome name for each  FASTA  file  will  be
              replaced  with the desired chromosome name in the file.  Every chromosome must have
              a corresponding line in the file.

       2.     A file with two columns per line, separated by white  space.   In  each  line,  the
              original  FASTA  chromosome  name  should be in column 1 and the desired chromosome
              name will be in column 2.  Not every chromosome needs to be listed, which  provides
              an easy way to change a few chromosome names.

       This  file can be combined with the --sort=names option, in which the order of chromosomes
       is
              that given in the file.  In this case, every chromosome must be listed in the file,
              and  for chromosome names that should not be changed, column 2 can be blank (or the
              same as column 1).  The option of a blank column 2 is allowed only when  specifying
              --sort=names,  because otherwise, the program cannot distinguish between a 1-column
              and 2-column names file.

       -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.

       -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) (default) 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

       -Q, --fastq
              Files are in FASTQ format

       -R, --revcomp
              Reverse complement all contigs

       -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)

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