In addition to papers, we consider high-quality, open-source software to be one of the primary scientific outputs of our work. Here you will find links to our lab’s software and a brief description of each tool.
Salmon is an accurate, fast and model-aware tool for transcript abundance estimation using RNA-seq data. It achieves its combination of speed and accuracy through a novel approach to read mapping (quasi-mapping) and a dual-phase inference algorithm.
Rapid sensitive and accurate transcriptome analysis via quasi-mapping.
Accurate, lightweight clustering of de novo transcriptomes using fragment equivalence classes.
Automated discovery of hierarchically-structured chromatin domains.
Maximum likelihood relatedness estimation from low-coverage sequencing data.
Sailfish is a tool for the rapid, alignment-free quantification of transcripts from RNA-seq