Wen-Bin Yu's repositories
covariants
Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
sarscov2phylo
Global phylogenies of SARS-CoV-2 sequences
ncov
Nextstrain build for novel coronavirus SARS-CoV-2
nextclade
Assign SARS-CoV-2 clades in the browser
picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
FixationSites
The application of R package sitePath on viruses.
Sequence-manipulation
A range of different perl scripts for manipulating sequences, conducting alignments, consensus sequences, changing formats
gatk
Official code repository for GATK versions 4 and up
wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
wuhan2020-timeline
记录自2019年12月起武汉新冠肺炎疫情进展的时间线。
sars-like-cov
This is a one-off Nextstrain build for SARS-like coronaviruses
GetOrganelle
Get organelle genomes from genome skimming data
megahit
Ultra-fast and memory-efficient (meta-)genome assembler
gffread
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
IMa3
IMa3
Beautiful-Visualization-with-R
《R语言数据可视化之美》配套代码
TBtools
GUI/CommandLine Tool Box for biologistists to utilize NGS data.
orthoscope
An automatic web tool for phylogenetic inference of bilaterian orthogroups under purposeful taxonomic sampling
BioGeoBEARS
BioGeography with Bayesian (and likelihood) Evolutionary Analysis with R Scripts
treeman
:deciduous_tree::man: An R package for manipulating phylogentic trees
whaleprep
Nextflow pipeline for preparatory analyses for Whale
PhyloSuite
PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
angsd
Program for analysing NGS data.
GetOrganelleComparison
Examples and comparisons
hyphy-gui
Desktop application for HyPhy
wgd
Python package and CLI for whole genome duplication analysis