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eXpress | Streaming fragment assignment for real-time analysis of sequencing experiments

Allows probabilistic assignment of ambiguously mapping sequenced fragments. eXpress can quantify the abundances of a set of target sequences from sampled subsequences. The software is suitable for many applications requiring probabilistic fragment assignment and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. It can be useful for resolving ambiguous mappings in high-throughput sequencing (HTS) based applications.

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eXpress classification

eXpress specifications

Unique identifier:
OMICS_01275
Software type:
Package/Module
Restrictions to use:
None
Input format:
Multi-FASTA+SAM/BAM
Output format:
XPRS
Computer skills:
Advanced
Stability:
Stable
Maintained:
No
Alternative name:
berkeley-express
Interface:
Command line interface
Input data:
A multi-FASTA file of target sequences and a file, multiple files, or a piped stream of alignments.
Output data:
Target abundancies, parameter estimates and count variance-covariance.
Operating system:
Unix/Linux, Mac OS, Windows
Version:
1.5.0
Source code URL:
https://pachterlab.github.io/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz

eXpress distribution

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eXpress support

Documentation

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Publications

Institution(s)

Department of Computer Science, University of California, Berkeley, Berkeley, CA, USA

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