Can Firtina's starred repositories
ann-benchmarks
Benchmarks of approximate nearest neighbor libraries in Python
Basecalling-comparison
A comparison of different Oxford Nanopore basecallers
pod5-file-format
Pod5: a high performance file format for nanopore reads.
mockcommunity
Long-read mock community experiments
read_until_api
Read Until client library for Nanopore Sequencing
DAMOV
DAMOV is a benchmark suite and a methodical framework targeting the study of data movement bottlenecks in modern applications. It is intended to study new architectures, such as near-data processing. Described by Oliveira et al. (preliminary version at https://arxiv.org/pdf/2105.03725.pdf)
squigulator
a tool for simulating nanopore raw signal data
kmer_models
Predictive kmer models for development use
minknow_api
Protobuf and gRPC specifications for the MinKNOW API
rapl-tools
Tools for monitoring CPU power with Intel's RAPL interface
RawHash
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)
ReadBouncer
Fast and scalable nanopore adaptive sampling
NanoSpring
Compressor for Nanopore Sequencing Reads
crisprDesign
Comprehensive design of CRISPR gRNAs for nucleases and base editors
DeepSelectNet
DeepSelecNet is an enhanced deep learning model to perform read classification for selective sequencing.
minimap2-fpga
An FPGA-accelerated version of minimap2