josiahseaman / MinION-Hackathon

Getting a Taxonomy Treemap streaming from a MinION device

MinION-Hackathon

Getting a Taxonomy Treemap streaming from a MinION device

Overall

We wanted to come up with a real-time platform to analyse (classify) and visualise a metagenome against ~500 fungal genomes.

This consists of:

• A subset of the NCBI taxonomy pulled by horrible_ncbi_taxonomy/ncbi_ids.Rmd which attempts to get a taxonomy (proxy for phylogeny) for the JGI fungal genomes
• A directory watcher (SimpleDirWatcher.jar) which triggers a bash script (do_metahack.sh) when new reads appear in the /input directory
• An analysis pipeline forked from do_metahack.sh which (at present) BLASTs reads against the 500 (actually 300) genome database
• A D3-based visualiser which uses a treemap paradigm to classify reads and cascade confidence information up the taxonomy to aggregate ID information by genus/family/phylum

Input

Sequence reads in FASTA

Output

Served to html:

Next steps

There's a google doc with more but:

• Programatically pull taxonomy more flexibly
• Debug D3 tree expansion
• Refine actual ID engine