Related Issues (20)
- finish out core genome finding algorithm for linear, circular, and multi-component graphs HOT 1
- Use degree >= 3 nodes for pre-indexing targets HOT 1
- Replace evidence named tuples with nested dictionaries HOT 1
- Stop putting kmer_counts datastructure into the metagraph
- https://julialang.github.io/PackageCompiler.jl/dev/index.html
- Stop running weave on development notebooks for documentation
- Use community detection for seperating out protein communities, genome communities HOT 7
- Use TSV for reading into & out of neo4j HOT 1
- Load host information into neo4j taxonomy db to improve viral filtering HOT 1
- When generating all possible AAmers, drop AAmers that start with stop codon
- get codespace env working again HOT 1
- Get jupyterlab templates working
- add jellyfish counting function HOT 1
- Switch to using static vectors for kmers instead of kmers.jl HOT 1
- Increase storage efficiency of genomes with Aeron's skipmer approach HOT 1
- Finish PoC joint-probility assembler + variant caller by passing my polished graphs into pggb/odgi+vg variant deconvolution flow HOT 2
- CAMI datasets to develop against
- Try dib-lab classification tools HOT 1
- Use conda.jl for downloading and managing containerized 3rd party software HOT 1
- Add documentation
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