liaoherui

StrainScan

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

VirStrain

An RNA virus strain-level identification tool for short reads.

GDmicro

GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data.

MetaComp

MAEP(Metagenomics Assembly Evaluation Pipeline). This pipeline is a new version of LAEP.

AnnoSINE_v2

Accelerating de novo SINE annotation in plant and animal genomes

StrainKmer

StrainKmer- an efficient and user-friendly tool for extracting viral strains' k-mers from raw sequencing data

GraphV

GraphV - An RNA virus strain-level identification tool using long reads and genome graph.

StrainDetect

StrainDetect is an online viral strain-level analysis tool based on VirStrain.

bioconda-recipes

Conda recipes for the bioconda channel.

CHERRY

Host prediction

StrainAMR

A learning-based tool to predict antimicrobial resistance and identify AMR-related genomic features from bacterial strain genomes

flask-vue-microblog

flask_microblog

flask_microblog

GFA-spec

Graphical Fragment Assembly (GFA) Format Specification

HOTSPOT

HOTSPOT is a hierarchical host prediction tool for plasmid contigs using Transformer.

IDMIL

IDMIL: An alignment-free interpretable deep multiple instance learning (MIL) for predicting disease from whole-metagenomic data

kraken2

The second version of the Kraken taxonomic sequence classification system

liaoherui.github.io

My blog - 2020 version

LRTK

A unified and versatile toolkit for analyzing Linked-Read sequencing data

PhaGCN

GCN classifier for phage taxanomy classification

PlantBind

A tool for predicting transcription factor binding sites in plants

PStrain

An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data.

quast

Genome assembly evaluation tool

README

README文件语法解读，即Github Flavored Markdown语法介绍

RNA_virus_detector

VirBot: a protein-based RNA virus detector for metagenomic data

SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs

StrainAnalyze

StrainAnalyze: a user-friendly bioinformatics pipeline used to analyze given identified bacterial strains in short reads.

strainest

StrainEst - abundance estimation of strains

ToolsCommandLines

All command lines running tools in VirStrain paper.

vg

tools for working with genome variation graphs