Software


Well-implemented awesomeness

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

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.

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RapMap

Rapid sensitive and accurate transcriptome analysis via quasi-mapping.

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RapClust

Accurate, lightweight clustering of de novo transcriptomes using fragment equivalence classes.

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Matryoshka

Automated discovery of hierarchically-structured chromatin domains.

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lcmlKin

Maximum likelihood relatedness estimation from low-coverage sequencing data.

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Sailfish

Sailfish is a tool for the rapid, alignment-free quantification of transcripts from RNA-seq

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