Lior Pachter's lab

http://math.berkeley.edu/~lpachter/software.html

Software developed in the Pachter group and still under active development in the group

• eXpress (2012) Streaming quantification for high-throughput sequencing.
• SysCall (2011) Distinguishing heterozygous sites from systematic error in high-thoughput sequenced reads
• Cufflinks (2010) Transcript assembly and abundance estimation for RNA-Seq (now a joint effort together with Cole Trapnell and the John Rinn Lab at Harvard University)
• MetMap (2010) Analysis of Methyl-Seq experiments

Software developed in the Pachter group but now maintained/developed elsewhere

• ReadSpy (2012) Assessment of uniformity in RNA-Seq reads (now supported by Valerie Hower and her group at the University of Miami)
• TopHat (2009) Splice junction mapper for short RNA-seq reads (now supported by Steven Salzberg and his group at Johns Hopkins University)
• FSA (2009) Fast Statistical Alignment (now supported by Robert Bradley and his group at FHCRC)
• MERCATOR (2004) Homology mapping (now supported by Colin Dewey and his group at the University of Wisconsin)
• VISTA (2000) Visualization tool for global alignments (now supported by Inna Dubchak and her group at the JGI)

Retired Software

These programs, originally developed in the Pachter group, are no longer under active development and are not being supported.

• AMAP (2007) Protein multiple alignment (recommended instead: FSA)
• GENEMAPPER (2006) Reference based gene annotation (recommended instead: an RNA-Seq experiment)
• MJOIN (2006) Neighbor joining with subtree weights (archived here)
• PARALIGN (2006) Alignment polytope construction (archived here)
• SLIM (2003) Minimum network design for optimizing the search space for pair hidden Markov models (archived here)
• SLAM (2003) Pairwise simultaneous alignment and gene finding (recommended instead: an RNA-Seq experiment)
• MAVID (2003) Multiple alignment of large genomic sequences (recommended instead: FSA)

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Submitted

L. Pachter, Models for transcript quantification from RNA-Seq, submitted.

In press

A. Roberts, L. Schaeffer and L. Pachter, Updating RNA-Seq analyses after re-annotation, in press.

M. Singer and L. Pachter, Bayesian networks in the study of genomewide DNA methylation, in press.

2013

A. Rahman and L. Pachter, CGAL: computing genome assembly likelihoods, Genome Biology, 14 (2013), R8.

2012

C. Trapnell, D.G. Hendrickson, M. Sauvageau, L. Goff, J.L. Rinn and L. Pachter, Differential analysis of gene regulation at transcript resolution with RNA-seq, Nature Biotechnology, advance online publication (2012).

S.A. Mortimer, C. Trapnell, S. Aviran, L. Pachter and J.B. Lucks, SHAPE-Seq: High throughput RNA structure analysis, Current Protocols in Chemical Biology, advance online publication.

A. Kleinman, M. Harel and L. Pachter, Affine and projective tree metric theorems, Annals of Combinatorics, advance online publication (2012).

A. Roberts and L. Pachter, Streaming fragment assignment for real-time analysis of sequencing experiments, Nature Methods, advance online publication (2012).

V. Hower, R. Starfield, A. Roberts, and L. Pachter, Quantifying uniformity in mapped reads, Bioinformatics, 28 (2012), 2680--2682.

L. Pachter, A closer look at RNA editing, Nature Biotechnology, 30 (2012), 246--247.

C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimentel, S.L. Salzberg, J.L. Rinn and L. Pachter, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, 7 (2012), 562--578.