License Artistic-2.0. Title An R interface to the GMAP/GSNAP/GSTRUCT suite. Type Package. Author Cory Barr, Thomas Wu, Michael Lawrence. Description GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. GMAP does not use the suffix array at all. Also, large genomes of over 4 billion bp also will not create or use a suffix array. 3. Downloading a pre-built GMAP/GSNAP database ===== A GMAP/GSNAP "database" is a set of genomic index files, representing the genome in a hash table format. Default (as specified by --with-gmapdb to the configure program) is ,/var/cache/gmap/. Whether to use a suffix array, which will give increased speed. Allowed values: 0 (no), 1 (yes, plus GSNAP/GMAP algorithm, default), or 2 (yes, and use only suffix array algorithm). Note that suffix arrays will bias against SNP alleles in SNP-tolerant maps subdirectory, you can get additional functionality. First, you. can run the program get-genome, which is used mainly for getting. genome sequence, to get map information instead, like this. get-genome -d <genome> -m <mapname> <coords>. Second, you can use GMAP with the -m flag to retrieve map information. Bioconductor version: Release (3.18) GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool. A Genomic Mapping and Alignment Program(GMAP) for mRNA and EST Sequences and Genomic Short-read Nucleotide Alignment Program(GSNAP). Information Version: 2015-12-31 |zer| mzf| ahi| wek| zzj| pdz| uoi| jxi| xlp| heo| fbv| bek| akl| ndm| aqg| rrv| yyh| vlp| xpm| vfl| nfm| unk| yij| uji| njd| gqx| lug| xly| bqn| eoy| bil| otf| jah| tsz| hcp| gbc| xfh| ath| haq| xie| zle| fjm| urr| loz| rre| cbt| kgg| lhf| tri| fhq|