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BABY GROOT & THE WASP


Overview

BABY-GROOT

BABY-GROOT is a dummer, smaller version of GROOT.

The main difference between BABY-GROOT and GROOT is that we no longer use exact alignments to detect variants. Instead, the seeded reads are used to create approximately weighted variation graphs. Expectation Maximization is then used to predict the most likely graph traversals based on the node weightings.

Another key difference is that the variation graphs are now indexed using LSH Ensemble instead of LSH Forest, which allows for containment search. This means that BABY-GROOT supports variable read length search queries.

These 2 changes have improved the efficiency of GROOT, such that we can now port it to WebAssembly (WASM) and have it run in a browser.

The WASP

The WASP part of this repo is a WebAssembly port of the BABY-GROOT command line tool, so that you can run it via a web app. This is currently hosted here. The cool thing about WASP (and web assembly in general) is that all the work is done client side - so no files leave your machine and you aren't reliant on a server.


Weighting variation graphs

The basic idea behind BABY GROOT is:

  • use sketches + an LSH Ensemble index to approximately map reads to variation graphs
  • use these mappings to create approximately weighted variation graphs (in GFA format)
    • we know a read approximately maps between nodes X and Z on a graph (with approx. error)
    • we used k-mer decomposition to generate a sketch
    • so nodes X through Z will have A k-mers, where A = length(X..Z) - k + 1
    • we can distribute A k-mers across nodes X, Y and Z
  • use EM to probabilistically determine the best paths through the weighted graphs
    • the best paths are equivalent to the gene variants in our sample
  • simplify the graph windowing
    • windows which have identical sketches are merged
    • instead of subpaths, have contained nodes (i.e. a sketch represents a set of nodes in the graph, which can come from multiple traversals)
    • no longer need offsets etc. - just weighting all nodes, regardless of sketch offset on a segment

Changes and new features since the GROOT publication

The original GROOT paper was published in Bioinformatics last year. BABY GROOT has seen a few changes:

  • replaced the indexing scheme (LSH Forest -> LSH Ensemble)
  • replaced existing hash functions
    • now only consider canonical k-mers
  • removed exact alignment step and BAM outputs
  • replaced align subcommand with sketch
  • replaced report subcommand with haplotype
  • output weighted GFA as the primary output
  • general code improvements and bug fixes
  • added support for Go modules and Go 1.13
  • added a WASM port
  • added a basic API so components can be more easily called from other Go programs

TODO

  • swap serialisation to messagepack (or maybe protobuf) from gob
  • improve WASM
    • currently only small index file sizes are supported before browser complains
    • add in more control over runtime parameters for BABY-GROOT

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A dummer, smaller version of GROOT

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