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 2016-06-09.

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