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...
deFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to red...
Novoalign is a program for mapping short reads from the Illumina/SOLiD sequencing platform(s) to a reference genome.
Package for aligning short reads to reference genomes
a frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each “child” sequence is considered to be stochastically derived from its more abundant “parent” sequence ...
Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of (~)11.4 million reads per hour.
RSEQtools includes a format specification for RNA-Seq data that provides confidentially-aware; data summaries as well as several tools for performing common analyses: expression measurements (e.g. RPKMs), creation of signal tracks, segmentation, annotation manipulations, etc.
A probabilistic framework is described to predict the alignment to the genome of all paired-end read transcript fragments in a paired-end read dataset. Starting from possible exonic and spliced alignments of all end reads, our method constructs potential splicing paths connecting paired...