Software

Here’s a list of software that I’ve been involved with creating, either directly (code I wrote) or indirectly (devised methods or supervised).

Bioinformatics

• fairy - fast approximate coverage for metagenomic binning.
• sylph - statistical ANI querying and profiling for metagenomic samples.
• floria - microbial strain phasing by flow-based MEC haplotyping.
• skani - fast and robust ANI calculation by sparse k-mer chaining.
• mora - strain-level read reassignment (written by Andrew Zheng).
• flopp - fast polyploid haplotype phasing for long-read data.
• OPERA-MS - hybrid metagenomic assembler for long and short-reads.

Misc.

• c2-CW - calculation of c2 invariant for graphs appearing in phi4 theory.

Trivia: my github name, bluenote-1577, is the record number for an album.