Genome assembly forensics: finding the elusive mis-assembly
We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describe...1920 days ago
JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wiki1504 days ago
Phytozome v12.1: plant science community hub for accessing palnts genomic data
Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub fo...1504 days ago
pggb: the pangenome graph builder
This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is l...1324 days ago
1219 days ago
Breedbase is a comprehensive breeding management and analysis software
Breedbase is a comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the...1209 days ago
The Snakemake Wrappers repository
The Snakemake Wrapper Repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows. More at https://github.com/snakemake/snakemake-wrappers984 days ago
976 days ago
RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold merging961 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements...934 days ago