Pinned Repositories
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scripts
00_Pangenome_Analysis
Pangenome Analysis Workflow with Prodigal and CD-HIT
12-trees
Variants analysis
A188Ref1
the process to build the first A188 reference genome
Ab10-Assembly
B73Ab10 genome assembly methods
adapt_PurgeHaplotigs_for_FALCONPhase
Convert output of purge haplotigs to format compatible with FALCON-Phase
adaptiPhy
This computational method has been published in BMC genomics as: "Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral"
admixturePipeline
A pipeline that accepts a VCF file to run through Admixture
HiC_tools
A collection of tools for Hi-C data analysis
maf2synteny
A tool for recovering synteny blocks from multiple alignment
bioCKO's Repositories
bioCKO/Tolypocladium_inflatum_paper
Scripts and customized scripts used in this paper
bioCKO/peer-review
A template for peer review of scientific publications
bioCKO/ThermoAlign
ThermoAlign: software for automated primer design
bioCKO/maize_v4_TE_annotation
scripts and intermediate files used to annotate TEs in Jiao et al.
bioCKO/Diploid-assembly
bioCKO/pyCircos
python Circos
bioCKO/HaplotigPlacement
bioCKO/ANGeS
Reconstruction of ancestral genome maps
bioCKO/JaltGenome
Raw scripts for de novo assembling a Jaltomata genome. Publication: Wu, M., Kostyun, J. and Moyle, L., 2018. Genome sequence of Jaltomata addresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae. Genome Biology and Evolution, evy274.
bioCKO/ncFANs
ncFANs: the first non-coding RNA Function Annotation Server
bioCKO/popgen_tutorial
bioCKO/Sliding_window_analysis
bioCKO/topaza_uce
all files and commands related to the topaza UCE allele phasing project
bioCKO/NucDiff
In-depth characterization and annotation of differences between two sets of DNA sequences
bioCKO/ZtoA_Heterozygosity
This repository contains scripts for studying heterozygosity on sex chromosomes and autosomes.
bioCKO/rnaed
RNA editing pipeline
bioCKO/RecoverY
K-mer based read classification for Y-chromosome specific sequencing and assembly
bioCKO/Exo70
Analysis of the Exo70 gene family and NLR-Exo70
bioCKO/jerboa
bioCKO/minimus3
bioCKO/hpcleap_dnds
Sliding window dN/dS vs. functional protein domain comparison tool. Given VectorBase gene id inputs it will aggregate various useful Bioinformatics information available, then allow the user to compare selective pressures acting along the protein sequence vs. an overlay of functional protein domain annotations.
bioCKO/Positive-Selection-with-HYPHY
Simple code for PS detection, can be used on several files
bioCKO/ak47
product for bioinfo
bioCKO/Harris_Kovacs_Londo
bioCKO/JaltPhylo
Raw scripts for the Jaltomata phylogenomics project. Publication: Wu, M., Kostyun, J. L., Hahn, M. W., & Moyle, L. C. (2018). Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance. Molecular Ecology, 27, 3301-3316.
bioCKO/kmer-extract-by-trigger-site
A script for extracting kmers (k base pair sized words) from fastq sequencing files after a specific trigger sequence.
bioCKO/haplotigtools
bioCKO/Handbook_of_biostatistic_R
:green_book:handbook of biostatistic and R
bioCKO/FASTKs
Pipeline for generate Ks plots of transcriptome data.
bioCKO/bioinformatics123