USeq Applications

USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations. USeq is under continuous development at the Huntsman Cancer Institute in the Utah Bioinformatics Shared Resource Center.

Novoalign Parser	Parses Novoalign files into center position binary PointData xxx.bar files for USeq analysis and xxx.bed files.
Novoalign Paired Parser	Parses paired Novoalign files into 12 column xxx.bed files. Useful for visualizing sequenced fragments.
Novoalign Bisulfite Parser	Parses Novoalign single and paired bisulfite sequence alignment files into xxx.bed and PointData file formats. Generates several summary statistics on converted and non-converted C contexts. Flattens overlapping reads in a pair to call consensus bps.
Novoalign Indel Parser	Parses Novoalign alignment files for consensus indels, something currently not supported by the maq apps. See Alleler app.

useq.sourceforge.net/applications.html