UnoSeqExpression profiling with next generation sequencing without a reference genome |
UnoSeqExpression profiling with next generation sequencing without a reference genome |
UnoSeq is a Java library to analyze next generation sequencing data (e.g. data generated by Illumina's mRNAseq method) and especially perform expression profiling in organisms where no well-annotated reference genome exists. The library can help you to extend your mRNAseq sequencing and transcription profiling approaches to any species you like.
The software is written in Java but to take full advantage of the library, you need to install some third-party tools for read mapping, read assembly and contig annotation. We recommend (and especially support) the use of Bowtie (for read mapping), Velvet (for read assembly) and BLAST (for contig annotation). Further information on how the pipeline works can be found in the detailed manual
If I can be of any help with Unoseq or your specific sequencing project, just contact me via fabian dot birzele at boehringer minus ingelheim dot com
20.03.2010: Our paper on Unoseq has been selected as a Featured Article by the Nucleic Acids Research Editorial Board. The published article can be found here (Open Access, so free for everyone who's interested)
06.02.2010: Our paper Into the unknown: Expression profiling without genome sequence information in CHO by next generation sequencing which shows one case study of the Unoseq pipeline is now accepted for publication in Nucleic Acids Research
01.02.2010: Version 1.0 of the UnoSeq pipeline is released.