A collection of scripts and notes related to genomics and bioinformatics

modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency

Subset of fast5 files contained in a fastq, BAM, or SAM file.

Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output

Wrapper to read fast5, slow5, blow5 and pod5 files.

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https…

Rust library to support interacting with Oxford Nanopore POD5 files

Synchronise Nanopore reads with a server.

Bob Loblaw's Law Blog Applauds Porexplorer

Dorado-basecalled reads improve old bacterial genome assembly

Wrapper to read fast5 and pod5 files.

Documentation for the https://github.com/JannesSP/read5 repository