Xiaoli Dong's repositories
pathogenseq
Pathogen whole genome sequence (WGS) data analysis pipeline
mag
Assembly and binning of metagenomes
monkeypox-nf
A monkeypox virus (MPXV) assembly pipeline using Nextflow for host-removal, reference-based assembly, and generation of sequence quality metrics for Illumina paired-end data using a shotgun metagenomic sequencing approach.
nf-flu
Influenza genome analysis Nextflow workflow
sequenoscope
A set of tools for working with adaptive sampling and comparison between treatment and control read sets
TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples