Stars
Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
Wally: Visualization of aligned sequencing reads and contigs
Fast alignment and preprocessing of chromatin profiles
This repository contains implementations and illustrative code to accompany DeepMind publications
Fast and accurate de novo assembler for long reads
Generate HCR-style Probe Pairs for mRNA visualization
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
GenMap - Fast and Exact Computation of Genome Mappability
A fast whole-genome aligner based on de Bruijn graphs
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Scaffolding genomes using synthetic long read clouds
A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Fast and memory-efficient sequencing error corrector
Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)
samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
Trawler is a integrated pipeline for the analysis of large scale chromatin-immunoprecipitation (ChIP) data and other large scale DNA-RNA datasets.
Species informed maximum a posteriori gene tree reconstruction
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0