Stars
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
AlleleFinder is a tool for identifying allele genes from polyploid genome.
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
One-step to Cluster and Visualize Gene Expression Matrix
aScan is a software tool for the determination of allele-specific-expression at the single individual level from matched RNA-Seq and genomic data.
Gene-based test of allele-specific expression without requiring haplotype information
Codes for pear haplotype genome and pangenome graph construction
phasing and Allele Specific Expression from RNA-seq
Read-based phasing of genomic variants, also called haplotype assembly
Train your AI self, amplify you, bridge the world
Earl Grey: A fully automated TE curation and annotation pipeline
A machine learning-based genotyping tool for structural variation in short reads
ctsa / svtools
Forked from hall-lab/svtoolsTools for processing and analyzing structural variants.
Structural variant and indel caller for mapped sequencing data
structural variant calling and genotyping with existing tools, but, smoothly.
LangChain Tools Collection
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
accurate LiftOver tool for new genome assemblies
Portable solution to generate genome alignment chains using lastz
CrossMap is a python program to lift over genome coordinates from one genome version to another.