Package: berkeley-express
Version: 1.5.3+dfsg-4
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 761
Depends: libbamtools2.5.3 (>= 2.5.3+dfsg), libboost-filesystem1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 7), libprotobuf32t64 (>= 3.21.12), libstdc++6 (>= 14)
Recommends: med-config
Section: science
Priority: optional
Homepage: http://bio.math.berkeley.edu/eXpress/index.html
Description: Streaming quantification for high-throughput sequencing
 eXpress is a streaming tool for quantifying the abundances of a set of
 target sequences from sampled subsequences. Example applications include
 transcript-level RNA-Seq quantification, allele-specific/haplotype
 expression analysis (from RNA-Seq), transcription factor binding
 quantification in ChIP-Seq, and analysis of metagenomic data. It is
 based on an online-EM algorithm that results in space (memory)
 requirements proportional to the total size of the target sequences and
 time requirements that are proportional to the number of sampled
 fragments. Thus, in applications such as RNA-Seq, eXpress can accurately
 quantify much larger samples than other currently available tools
 greatly reducing computing infrastructure requirements. eXpress can be
 used to build lightweight high-throughput sequencing processing
 pipelines when coupled with a streaming aligner (such as Bowtie), as
 output can be piped directly into eXpress, effectively eliminating the
 need to store read alignments in memory or on disk.
 .
 In an analysis of the performance of eXpress for RNA-Seq data, it was
 observed that this efficiency does not come at a cost of accuracy.
 eXpress is more accurate than other available tools, even when limited
 to smaller datasets that do not require such efficiency. Moreover, like
 the Cufflinks program, eXpress can be used to estimate transcript
 abundances in multi-isoform genes. eXpress is also able to resolve
 multi-mappings of reads across gene families, and does not require a
 reference genome so that it can be used in conjunction with de novo
 assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model
 is based on previously described probabilistic models developed for
 RNA-Seq but is applicable to other settings where target sequences are
 sampled, and includes parameters for fragment length distributions,
 errors in reads, and sequence-specific fragment bias.
 .
 eXpress can be used to resolve ambiguous mappings in other
 high-throughput sequencing based applications. The only required inputs
 to eXpress are a set of target sequences and a set of sequenced
 fragments multiply-aligned to them.  While these target sequences will
 often be gene isoforms, they need not be. Haplotypes can be used as the
 reference for allele-specific expression analysis, binding regions for
 ChIP-Seq, or target genomes in metagenomics experiments. eXpress is
 useful in any analysis where reads multi-map to sequences that differ in
 abundance.
