I lead technical teams in biotech and write software for new genomics technologies. At Fulcrum Genomics you'll find me building tools and leading others in the fields of oncology, cell & gene editing, and precision medicine all while ensuring we deliver high-quality services to our clients and partners.
| Project | Stack | Install | What it does |
|---|---|---|---|
| bamby |  |
 |
Group BAM records into read groups by the value of a tag. |
| chaff | |
|
Flag somatic calls that are library-prep artifacts. |
| chum | |
|
Evaluate baits in a hybrid selection panel. |
| krak | |
|
An addicting set of Kraken-enhancing tools. |
| unmux | |
|
Parse and demultiplex records, splitcode-style. |
| vartovcf | |
|
Stream VarDict variants into VCF v4.2. |
| annatar | |
 |
Convert a VCF of single cells to an AnnData h5ad. 78D5 |
| streampile | |
 |
Forward-only pileups of SAM, BAM, and CRAM. |
| spillsort | |
 |
Sort more items than fit in memory. |
| neodisambiguate |  |
|
Disambiguate reads mapped to multiple references. |
| bedspec |  |
 |
An HTS-specs compliant BED toolkit. |
| captainslog | |
 |
Typed dataclasses for Riker and Picard metrics. |
| cellme | |
 |
Make a truth-track VCF of a cell line's known mutations. |
| pybgzf | |
 |
Streaming BGZF with on-the-fly tabix and CSI indexing. |
| typeline | |
 |
Dataclasses to delimited text, round-trip with types. |
| ebs-autoscale |  |
Autoscaling EBS-backed scratch storage on AWS. |
