Benchmark basecallers for nanopore sequencing
Description
Assess accuracy of available basecallers. Planning on adding support for many of the following: DeepNano, BasecRAWller, Nanonet/Albacore/Scrappie
Basecallers initially included for testing:
- Nanocall (https://github.com/mateidavid/nanocall)
- Chiron (https://github.com/haotianteng/Chiron)
- Metrichor (original basecaller from ONT)
Requirements
- Python 3 and Biopython
- BWA (https://github.com/lh3/bwa), for reference genome alignment
- Alfred (https://github.com/tobiasrausch/alfred), for gathering alignment statistics
- Japsa (https://github.com/mdcao/japsa), for gathering alignment statistics