A tool for somatic structural variant calling using long reads

Structural variant filtering and anlaysis of Nanopore human WGS data.

RNA modifications detection from Nanopore dRNA-Seq data

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

Plotting scripts for long read sequencing data

MuTect -- Accurate and sensitive cancer mutation detection

Pilon is an automated genome assembly improvement and variant detection tool

Generates plots reporting on nanopore runs

Nanopolish wrapper for SGE

An Oxford Nanopore Basecaller

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

A single molecule sequence assembler for genomes large and small.

BWT-based index for graphs

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which…

tools for working with genome variation graphs

Flexible genotype query among 30,000+ samples whole-genome

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

MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities

Models and APIs for Genomic data. RETIRED 2018-01-24

K-mer counting contest

Implementation of the multiple sequential markovian coalescent

Convenience function for quick and dirty data analysis

Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

Tools for working with SAM/BAM data

A De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework

BEETL

in-memory k-mer counting

🔬 Assemble large genomes using short reads