WhopGenome: High-speed processing of whole-genome VCF-format variation data,
FASTA-format sequence data and several alignments formats
WhopGenome's provides very fast access to whole genome, population scale variation data
from VCF files and sequence data from FASTA-formatted files.
It also reads in alignments from FASTA, Phylip, MAF and other file formats.
Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data
from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
||R (≥ 1.8.0)
||RMySQL, DBI, AnnotationDbi
<ulrich.wittelsbuerger at uni-duesseldorf.de>
||GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
||This package uses zlib, Tabix, bgzf and faidx. Zlib by
Jean-loup Gally <firstname.lastname@example.org> and Mark Adler
<email@example.com>, uses the Zlib licence. Tabix and
FaIdx by Heng Li <firstname.lastname@example.org> use the MIT licence. BGZF as
by Bob Handsaker and modified by Heng Li uses the MIT licence.
Anything else was written entirely by Ulrich Wittelsbuerger.
All third-party code has been slightly modified to conform to R
package development requirements such as removal or replacement
of printf, fprintf on stderr and functions that would terminate
a running R session by R-supplied equivalents as well as
modifications that eliminate most compiler warnings.