Pinned Repositories
00_in-situ_GeneCoverage
Workflow to calculate ANIr and sequence coverage (depth and breadth) of genome(s) / MAG(s) from metagenomes by gene, intergenic region, contig, and whole genome.
Amplicon-data-processing
Pipeline for 16S rRNA amplicon data analysis and infer 16S rRNA sequences from metaG using parallel-meta suite
ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
cactus
Official home of genome aligner based upon notion of Cactus graphs
ColabFold
Making Protein folding accessible to all!
emapper2gbk
Convert GFF, fastas, annotation table and species name into Genbank.
FastAAI
genome-scale-models
Genome scale metabolic models in SBML format
genome_assembly_tools
List of genome assembly tools
utguang's Repositories
utguang/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
utguang/cactus
Official home of genome aligner based upon notion of Cactus graphs
utguang/ColabFold
Making Protein folding accessible to all!
utguang/emapper2gbk
Convert GFF, fastas, annotation table and species name into Genbank.
utguang/FastAAI
utguang/genome_assembly_tools
List of genome assembly tools
utguang/GenoVi
GenoVi, an automated customizable circular genome visualizer for bacteria and archaea
utguang/ggcoverage
Visualize and annotate genomic coverage with ggplot2
utguang/ggforce
Accelerating ggplot2
utguang/ggtree
:christmas_tree:Visualization and annotation of phylogenetic trees
utguang/github-slideshow
A robot powered training repository :robot:
utguang/gRodon2
utguang/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
utguang/islandpath
IslandPath standalone software
utguang/mag
Assembly and binning of metagenomes
utguang/msamtools
Metagenomics-related extended functionalities to samtools
utguang/nov-fams-pipeline
utguang/Paper-code
Codes used in papaer "Sustained N2O reduction at acidic pH"
utguang/phyloFlash
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
utguang/picrust2
Code, unit tests, and tutorials for running PICRUSt2
utguang/PLASMe
utguang/PlasmidHunter
This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.
utguang/plaSquid
Nextflow pipeline for plasmid detection and classification from metagenomic data
utguang/proteinfold
Protein 3D structure prediction pipeline
utguang/quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
utguang/RecruitPlotEasy
A tool for interactive Recruitment Plot generation and viewing
utguang/rrap
Metagenomic Read Recruitment Pipeline
utguang/SMAG
Soil microbial dark matter mining based on genome-resolved metagenomics
utguang/TOmicsVis
Transcriptomics Visualization R package.
utguang/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction