Selected software
sourmash
Python and Rust
Sketch-based search and comparison of genomic and metagenomic data. Contributor to the v4 line and co-author of the software paper.
cifiasm
Python
Assembly and scaffolding workflow for a combined HiFi and CiFi library: one prep instead of three sequencing platforms.
cifi-toolkit
C++ and Python
Makes CiFi sequencing data usable by the scaffolding and contact-map tools that already exist.
kSpider
C++
Pairwise clustering of sequence collections from k-mer sketches, in a single pass.
DBRetina
Python and C++
Gene-set overlap as a network, for finding structure across thousands of published sets at once.
kProcessor
C++
A framework for indexing and processing k-mers, with Python bindings.
sourmash plugins
C++ and Python
Plugins I wrote or contributed to that extend sourmash.
denovo-rnaseq
Python
De novo assembly, differential expression, and annotation as one workflow.