bioCKO's repositories
A188Ref1
the process to build the first A188 reference genome
Ab10-Assembly
B73Ab10 genome assembly methods
ADratio
Classifying sex-linked and autosomal scaffolds using allele-depth ratios computed from pileup data
aspergillus_ps
In this repository we describe the workflow followed to process and analyze the data of the study "Aspergillus fumigatus versus Genus Aspergillus: Conservation, adaptive evolution and specific virulence genes".
Circos-Pipeline
circos pipeline
Comparative-transcriptome-analysis
Analysis of RNA-Seq data accompanying the project titled 'Comparative transcriptome profiling of human and pig intestinal epithelial cells after porcine delta coronavirus infection'
CSA2.6
Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes
DLEPS
A Deep Learning based Efficacy Prediction System for drug discovery
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)
GenomicsOfLarvalMalnutrition
the statistical tests in the GWAS process
guppy_convergence
Associated data and scripts for "Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies""
merqury
k-mer based assembly evaluation
microbiome_helper
A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
ngs-protocols
Scripts to run several protocols to process and analyze Next-Generation Sequencing data
programmer_math
程序员的数学三本书
pseudofinder
Detection of pseudogene candidates in bacterial and archaeal genomes.
RACCROCHE
Ancestral flowering plant genomes reconstruction
SolsexGenome
This is the scripts we used for performing the analyses in our research work on Solanum appediculatum genome and identification of sex determination region
stickleback_adaptive_radiations
Scripts associated with Magalhaes and Whiting et al 2020
TADEvoDrosophila
Code for TAD_SV project
vole_genome_analysis
Material for the analysis of Microtus whole genomes
yhaplo
Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men