Chenglin20170390

pantera

Identification of transposable element families from pangenome polymorphisms

GenomeDelta

Library-free horizontal transfer detection, with a focus on transposable element invasions

pggb

the pangenome graph builder

Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

fastDFE

Fast and flexible inference of the distribution of fitness effects (DFE), VCF-SFS parsing with ancestral allele and site-degeneracy annotation.

genomics_general

General tools for genomic analyses.

hybrid_origin_of_the_potato

Potato_C88

Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning

assembly-annotation-pipeline

Plant genome assembly and annotation pipeline using snakemake

kmerDedup

Reduce genome assembly redundancy using shared mapped k-mer method.

pyfastani

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

vg

tools for working with genome variation graphs

phased-assembly-check

ElConcatenero

gatk

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository