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gmap_build - Online in the Cloud

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This is the command gmap_build that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 2015-12-31.

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.

-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

Use gmap_build online using onworks.net services


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