lizhizhong1992's repositories
genomics_general
General tools for genomic analyses.
AliTV
Visualize whole genome alignments as linear maps
Assembly
Pipelines and scripts related to genome assembly, annotation, and analysis
ASTRID
Fast, accurate species tree estimation.
blobtools
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
cgat-apps
cgat-apps repository
Coilia_nasus_parallel_evolution
Scripts used in parallel evolution analysis of Coilia nasus
course-linux-command-line-bash-scripting-metacentrum
Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple osX, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.
dDocent
a bash pipeline for RAD sequencing
DiscoSnp
DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.
ENMwizard
Advanced Techniques for Ecological Niche Modeling Made Easy
FastqSifter
Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)
Flye
De novo assembler for single molecule sequencing reads using repeat graphs
Maxent
Maximum entropy modelling of species geographic distributions.
Maya
Maya's Master Thesis
plotHicGenome
The tools are used for displaying hic signal of genome
pyscript-bio
生物信息学python代码，专注于重测序文本计算、处理
reconstruct_mito_genome
Full *dis* assembler for plant mitochondrial genomes
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
shiny_popgen
Shiny apps for teaching Population Genetics
structure-multi-pbspro
Set of scripts to run STRUCTURE in parallel on computing grids like MetaCentrum. Scripts are designed for grids and clusters using PBS Pro, but can be easily adopted for another queue system.
syntenet
An R package to infer and analyze synteny networks from protein sequences
tutorials
Tutorials on phylogenetic and phylogenomic inference