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
