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