yibo dong's repositories
multi-ploidSNPs
a GBS-based pipeline for calling SNPs from a group of samples with different ploidy.
3GenomeSNP_pipeline
A pipeline to seperate NGS sequencing data into chloroplast, mitochondria and nuclear genomes, and then call SNPs in the 3 genomes respectively.
BMGAP
The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples
Cecret
Nextflow workflow for our analysis of SARS-COV-2
enzyme_cutting_simulation_scripts
These scripts are used for silic simulation analysis of enzyme-cutting-genome
NCHHSTP-DTBE-Varpipe-WGS
This repository contains an analysis pipeline developed to characterize WGS output
PhaME
Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
Roary
Rapid large-scale prokaryote pan genome analysis
snakemake_nextflow_wdl
simple comparison of snakemake, nextflow and cromwell/wdl
snp-sites
Finds SNP sites from a multi-FASTA alignment file
Team1
Team Leaders: Anujit Sarkar, Agaz Wani
Unicycler
hybrid assembly pipeline for bacterial genomes