chaigsh's repositories
Basecalling-comparison
A comparison of different Oxford Nanopore basecallers
bazam
A read extraction and realignment tool for next generation sequencing data
Bismark
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
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
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
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
pysradb
Package for fetching metadata and downloading data from SRA
SquiggleKit
SquiggleKit: A toolkit for manipulating nanopore signal data
tombo
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.