embed_fast5

Embed fast5 signal files with a correctly formatted kmer to event alignment given the nucleotide sequence and a model file

Dependencies

• Boost >= 1_69_0
• HDF5 (sudo apt-get install libhdf5-dev)
• Eigen (sudo apt-get install libeigen3-dev)
• HTSLIB >= 1.9
• cmake >= 3.15

Install

• Recommend using Docker image ucscbailey/embed:1.0.0

Install instructions

• git clone --recursive https://github.com/adbailey4/embed_fast5.git
• cd embed_fast5
• pip install -e .
• pytest

Debugging

If the install instructions do not work, check out this Dockerfile