Open source code for AlphaFold 2.

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Single-cell analysis in Python. Scales to >100M cells.

RNAseq analysis notes from Ming Tang

Python library to facilitate genome assembly, annotation, and comparative genomics

python module to plot beautiful and highly customizable genome browser tracks

ChIP-seq analysis notes from Ming Tang

Phylogenetic orthology inference for comparative genomics

Tools to process and analyze deep sequencing data.

Fast genome-wide functional annotation through orthology assignment

Gene cluster comparison figure generator

Bioinformatics code libraries and scripts

Tools for fast and flexible genome assembly scaffolding and improvement

An accurate GFF3/GTF lift over pipeline

ENCODE ATAC-seq pipeline

General tools for genomic analyses.

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Eukaryotic Genome Annotation Pipeline

Tool to plot synteny and structural rearrangements between genomes

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

GFF and GTF file manipulation and interconversion

ENCODE ChIP-seq pipeline

Long read based human genomic structural variation detection with cuteSV

An overview of all nanopack tools

This Snakemake pipeline implements the GATK best-practices workflow

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries