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GMAP_GSNAP v2012.11.21 (Genomic Mapping and Alignment Program) for mRNA and EST Sequences)

This version should be considered a beta version. All reported fatal bugs have been resolved, but it is possible other bugs could be reported. For the last known stable version, please go to the archive and download version 2012-07-20.

Major changes to GSNAP and GMAP:

Enabled alignment for circular chromosomes
Favoring shorter introns at ends
Trimming query N's at ends of alignments, so they do not imply a false extension
Minor improvements in alignment accuracy
In SNP-tolerant alignment, removed more biases that favor the reference genome over the alternate genome
In SNP-tolerant alignment, fixed cases where genomic Ns were being treated as wildcard characters
Added --novelend-splicedist to control allowed splice distance at ends for novel splicing
Added --append option to append results to output files when --split-output is used
Added --md-lowercase-snp to print allelic differences as lower case when they correspond to known variants
Added --force-xs-dir flag to eliminate XS:A:? fields in SAM output
Added XW and XV flags to SAM output when SNP-tolerant alignment is used
For --pairalign mode in GMAP, multiple pairs of sequences can be provided

Source Files

Filename Size Changed Actions
GMAP.spec 2.99 KB Download File
gmap-gsnap-2012.11.21.tar.bz2 2.85 MB Download File

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