Dr. Chaochun Wei, Department of Bioinformatics and Biostatistics

Software

Genomics
• CTF: a Conditional random field based Transcript factor binding site Finding system
• MOST+: A motif finding system combing genomic sequence and heterogenous genome-wide signatures
• ALTSCAN: ALTernative Splicing SCANner
• Superstable Elements found in 10 human genomes

Metagenomics, Metatranscriptomics
• NeSSM: Next generation Sequencing Simulator for Metagenomics
• NeSSMt: Next generation Sequencing Simulator for Metatranscriptomics
• PaSS: PacBio Sequencing Simulator
• MetaBinG: an ultra-fast metagenomic sequence classification system using graphic processing units (GPUs)
• MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms
• CDKAM: a taxonomic classification tool using discribminative k-mers and approximate matching strategies (also called MetaBinG3: MetaBinG for 3rd-generation sequencing long reads)
• MetaAll: Metagenomics and Metatranscriptomics data analysis system
• MetaCSST: MetaGenomic Complex Sequencing Scanning Tool
• CTCM: Classify Transcripts from Coral Metatranscriptome

Pan-genome analysis
• RPAN: Rice Pan-genome Browser for 3K rice genomes
• EUPAN: a toolbox for Eukaryote Pan-genome ANalysis
• HUPAN: a pan-genome analysis pipeline for human genomes
• PPanG: a precision pangenome browser integrating individual genomes and their graph-based pangenome

Applied Genomics
• GLAPD: whole genome based LAMP primer design for a set of target genomes

   

©2010 Chaochun Wei