Starred repositories
Genome-wide Efficient Mixed Model Association
Efficient Permutation-based GWAS for Normal and Skewed Phenotypic Distributions
A curated list of practical guide resources of LLMs (LLMs Tree, Examples, Papers)
Phylogenetic orthology inference for comparative genomics
This is a workflow that combines multiple software, mainly for whole genome annotation of eukaryotes.
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
A single molecule sequence assembler for genomes large and small.
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
A rapid and accurate ensemble pipeline for graph-based variant genotyping with lower depth of short reads
Python package with helper tools for the nf-core community.
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Alignment-free genotyper for SNPs and short indels, implemented in Python.
Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
Construct and Analyze the North American Vitis pangenome
SMC++ infers population history from whole-genome sequence data.
Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.
displays multiple genomic sequences in the form of a tube map
This is a method to find telomeres and centromeres in plants.
Official home of genome aligner based upon notion of Cactus graphs