chen318liang

100-gcc-tips

A collection of gcc tips. 100 maybe just mean many here.

abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

awesome-cheatsheets

超级速查表 - 编程语言、框架和开发工具的速查表，单个文件包含一切你需要知道的东西 :zap:

Basecalling-comparison

A comparison of different Oxford Nanopore basecallers

free-programming-books

:books: Freely available programming books

Gut-Metagenome-Pipeline-Based-on-Nanopore-Sequencing

NextPolish

Fast and accurately polish the genome generated by noisy long reads.

OrthoFinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

chen318liang/Gut-Metagenome-Pipeline-Based-on-Nanopore-Sequencing

chen318liang/abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

chen318liang/antismash_parsing

A collection of simple python scripts for extracting info from antismash gbk files

chen318liang/BiG-MAP

chen318liang/bioinfo-notebook

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

chen318liang/blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

chen318liang/cactus

Official home of genome aligner based upon notion of Cactus graphs

chen318liang/carveme

CarveMe: genome-scale metabolic model reconstruction

chen318liang/clinker

Gene cluster comparison figure generator

chen318liang/CoverM

Read coverage calculator for metagenomics

chen318liang/dotPlotly

Generate an interactive dot plot from mummer or minimap alignments

chen318liang/examples

Microbiome Informatics - API and service usage examples

chen318liang/genomes-pipeline

MGnify genome analysis pipeline

chen318liang/inStrain

Bioinformatics program inStrain

chen318liang/kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

chen318liang/lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.

chen318liang/MagCluster

Magnetosome gene cluster annotation, screening and visualization tool

chen318liang/MetaboAnalystR

R package for MetaboAnalyst

chen318liang/micom

Python package to study microbial communities using metabolic modeling.

chen318liang/multismash

A workflow and scripts for large-scale antiSMASH analyses

chen318liang/spatial-bonemarrow-atlas

This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Proteomic Profiling Reveals the Cellular Composition and Spatial Organization of the Human Bone Marrow Microenvironment"

chen318liang/SVanalyzer

Tools for the analysis of structural variation in genomes

chen318liang/svmu

A program to call variants from genome alignment

chen318liang/syri

Synteny and Rearrangement Identifier

chen318liang/Tax4Fun2

chen318liang/The-gut-microbiome-and-longevity-project-GMLP

chen318liang/trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

chen318liang/vamb

Variational autoencoder for metagenomic binning

chen318liang/viralFlye

scripts for potential viral+metaflye paper

chen318liang/wlab_antismash