jinhao94's starred repositories
PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
referenceseeker
Rapid determination of appropriate reference genomes.
Metatranscriptome-Workshop
Metatranscriptomics Tutorial
pantagruel
a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
RabbitTClust
RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches
DMP
Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.11.27.401125v1 and full data can be requested from EGA (https://ega-archive.org/studies/EGAS00001005027) and Lifelines biobank (https://www.lifelines.nl/researcher)
COPD_multiomics
This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interaction in Chronic Obstructive Pulmonary Disease'.
score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
Waters2mzML
Waters2mzML converts & subsequently annotates Waters .raw MSn data (both MSe & DDA) into functional .mzML files. Obtained .mzML files can be processed in MZmine 3. It would be interesting to see if it works for all Waters .raw data and other processing streamlines.