This repository contains data indexes from NIST's Genome in a Bottle project.

Human Pangenome Reference Consortium - HG002 Data Freeze (v1.0)

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

A simple tool for extracting reads from Oxford Nanopore fast5 files

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Nanopore demultiplexing, QC and alignment pipeline

Squiggle and Sequence Plotter in Python

Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.

slow5lib is a software library for reading & writing SLOW5 files.

Useful bash one-liners for bioinformatics.

Benchmarking programming languages/implementations for common tasks in Bioinformatics

minimal example implementations for bioinformatics workflow managers

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Adaptive Banded Event Alignment

A streaming method for mapping nanopore raw signals

A PyTorch Basecaller for Oxford Nanopore Reads

Research release basecalling models and configurations

NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files

Benchmarking of long-read assembly tools for bacterial whole genomes

Geni users to create Hadoop and Spark profile on CloudLab

A C++ header-only library for reading Oxford Nanopore Fast5 files

A basecaller for Oxford Nanopore Technologies' sequencers

A comparison of different Oxford Nanopore basecallers

Supporting Hierarchical Data Format and Rich Parallel I/O Interface in Spark

HDF5 for Python -- The h5py package is a Pythonic interface to the HDF5 binary data format.

Specifications for PacBio® native file formats

Makes distinct TSS of each gene from a Gencode annotation

Oxford Nanopore's Basecaller

Pod5: a high performance file format for nanopore reads.