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gmap_build - Tool for genome database creation for GMAP or GSNAP


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


gmap_build: Builds a gmap database for a genome to be used by GMAP or GSNAP. Part of GMAP
package, version 2015-12-31.

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


-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.

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

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

Obsolete options:
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

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