Stars
UCSC Genome Browser source. "beta" is released version / "master" is testing.
Long read production pipelines
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like…
Single-cell analysis in Python. Scales to >100M cells.
A pipeline to investigate horizontal gene transfer from NGS data
Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
Single cell RNA sequencing analysis course
Official home of genome aligner based upon notion of Cactus graphs
Making Protein folding accessible to all!
ATAC-seq peak-calling and QC analysis pipeline
Analysis of convergence between organismal traits and DNA/protein sequences
biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
A list of interesting genome browser and genome visualization programs
Extract 3D contacts (.pairs) from sequencing alignments
📊 A universal enrichment tool for interpreting omics data
🚥 Visualizing publication-quality multiple sequence alignment using ggplot2
Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.