Simple demonstration of using spatial indexes (here kd-trees) to approximately map nanopore squiggle reads
Python Shell
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
ecoli
models
LICENSE
README.md
blogpost-runs.sh
ecoli.fa
em_rescale.py
fast5.py
index-and-map.sh
mapread.py
poremodel.py
readtofasta.py
spatialindex.py

README.md

Simple Squiggle Pseudomapper

Simple demonstration and testbed of using spatial indexes (here kd-trees) to approximately map nanopore squiggle reads.

Running the index_and_map.sh script provides a quick demonstration, indexing the reference sequence of an ecoli strain and approximately mapping 10 reads of older and newer nanopore reads to the reference.

Ideas are discussed on the Simpsonlab blog post, http://simpsonlab.github.io/2015/12/18/kdtree-mapping/