Projects

Lorikeet

Lorikeet is a variant calling, strain genome resolving, and microdiversity assessment algorithm for metagenomics. The variant calling algorithm Lorikeet uses is a full re-implementation of the GATK HaplotypeCaller algorithm in Rust. It is both faster and easier to use with almost identical results. Lorikeet can make use of both long and short reads simultaneously, handling both the mapping and parallelization of the analysis of multiple genomes with minimal effort required of the user.

Rosella

Rosella is a metagenomic binning algorithm written in Rust and Python. It makes use of UMAP and HDBSCAN to generate metagenomic assembled genomes from metagenome assemblies. It can both map and calculate coverage information for assemblies and is capable of handling and long and short reads simultaneously.

Aviary

Aviary is a modular and easy to use to complete metagenomic workflow written in python wrapping around snakemake. Aviary is capable of handling hybrid assembly of long and short reads from various sequencing platforms. Additionally, Aviary performs robust binning using a large suite of metagenomic binners and ensemble binning. Finalized bins are also assessed for quality using CheckM, and assigned taxonomic ranks using GTDB-tk. Various other statistics are also reports like recovered diversity at various steps using SingleM and coverage statistics using CoverM

ChIP-R

ChIP-R is a reproducibility assessment algorithm for ChIP-seq and ATAC-seq data. It allows the testing of multiple replicates at a time allowing users to generate finalized sets of high confidence ChIP-seq and ATAC-seq peaks with ease. The publication can be found here

Contributions

• Kingfisher
• CoverM
• Galah

Hobby side projects

Nymph

Non-negative matrix factorization in rust