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Using Deep Learning to predict gene annotations
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Tutorials for bioinformatics and data analysis related to landscape genomics
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.
Code to compute the XP-CLR statistic to infer natural selection
Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
SALSA: A tool to scaffold long read assemblies with Hi-C data
A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
Transposable element polymorphism identification
Piranha is a peak-caller for CLIP- and RIP-seq data
🏊 Individual-Level, Summary-Level and Single-Step Bayesian Regression Models for Genomic Prediction and Genome-Wide Association Studies
🚴 Kinship Adjusted Multi-Loci Best Linear Unbiased Prediction
RAxML Next Generation: faster, easier-to-use and more flexible
A visualization grammar and GPU-accelerated toolkit for genomic data
A rapid and accurate ensemble pipeline for graph-based variant genotyping with lower depth of short reads
A tool for quick and accurate calculation of syntenic diversity.
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!