User-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual...
Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that expl...
Given gene annotation the major questions addressed by the package are: prediction of alternative exons in a single condition / cell sample, prediction of differential alternative exons between two conditions / cell samples, quantification of alternative splice forms in a single conditi...
Patman searches for short patterns in large DNA databases, allowing for approximate matches. It is optimized for searching for many small pattern at the same time, for example microarray probes.
CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework cal...