bioCKO's repositories
00_Pangenome_Analysis
Pangenome Analysis Workflow with Prodigal and CD-HIT
AMPRIL-genomes
scripts for the project of seven thaliana genomes assembly
Atlantic_herring_SDR
This repository provides codes and analyses pipeline for discovery of Atlantic Herring sex chromosome
Celligner_ms
Code related to the Celligner manuscript
centroFlye
An algorithm for centromere assembly using long error-prone reads
cruk-summer-school-2020
Web-site for the 2020 CRUK CC Bioinformatics Summer School (Held virtually)
ForwardGenomics
Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework
HalfDeep
Automated detection of intervals covered at half depth by sequenced reads.
HAST4TGS
A version of HAST for TGS long reads, fast and memory-effiective trio-binning.
Lace
Building SuperTranscripts: A linear representation of transcriptome data
postgap
Linking GWAS studies to genes through cis-regulatory datasets
PPGfinder
Discover processed pseudogene from long structural variations.
PrimerServer2
PrimerServer2: a high-throughput primer design and specificity-checking platform
PseudoHunter
Identification of pseudogenes based on pairwise comparison between genomes
Psyllid_chromosome_assembly
Scripts used for the chromosome-level genome assembly of the hackberry petiole gall psyllid (Pachypsylla venusta)
REDItools
REDItools are python scripts to investigate RNA editing at genomic scale.
RFO
A new approach for orthologs and lineage-specific genes assignment based on reference-free whole-genome alignment
SCALE
Allele-Specific Expression by Single-Cell RNA Sequencing
snakemake-sex-chr
A snakemake pipeline for detection of sex-linked regions from wgs sequencing data.
snp_hunter
Search transcriptome assemblies for transcripts that might represent sex-specific genes
svmu
A program to call variants from genome alignment