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basecalling-comparison

A comparison of different Oxford Nanopore basecallers

bazam

A read extraction and realignment tool for next generation sequencing data

bioinformatics-training

Bioinformatics training resources

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

circleseq

custom_scripts

In the process of data analysis, it is always necessary to customize scripts to accomplish specific tasks.

deepmod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications

deeptools

Tools to process and analyze deep sequencing data.

fast5tools

Tools for working with fast5 files (nanopore data).

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fastqc

A quality control analysis tool for high throughput sequencing data

graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html

guideseq

Analysis pipeline for the GUIDE-seq assay. For news, see:

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

introduction-to-b-g

share materials with students

mecat2

merip_reanalysis_scripts

Scripts for paper entitled "Limits in the detection of m6A changes using MeRIP/m6A-seq

metaqc

MetaQC: the MeRIP-seq data analysis and quality control toolkit

methylkit

R package for DNA methylation analysis

nanor

R package for user-friendly analysis and comparison of ONT data

nanoraw

Genome guided re-segmention and visualization for raw nanopore sequencing data.

necat

Nanopore data assembler

openconnect-gui

Graphical OpenConnect client (beta phase)

paddle

PArallel Distributed Deep LEarning （PaddlePaddle核心框架，高性能单机、分布式训练和跨平台部署）

pbsim-pacbio-simulator

This is an updated mirror of the original PacBio Read Simulator

poretools

a toolkit for working with Oxford nanopore data

prinseq-plus-plus

parallel c prinseq

pypore

Tools used to analyze data from nanopore-based experiments.

pysradb

Package for fetching metadata and downloading data from SRA

squigglekit

SquiggleKit: A toolkit for manipulating nanopore signal data