fmarletaz's Stars
fethalen/Patchwork
Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
tobiasrausch/wally
Wally: Visualization of aligned sequencing reads and contigs
haowenz/chromap
Fast alignment and preprocessing of chromatin profiles
google-deepmind/deepmind-research
This repository contains implementations and illustrative code to accompany DeepMind publications
Nextomics/NextDenovo
Fast and accurate de novo assembler for long reads
rwnull/insitu_probe_generator
Generate HCR-style Probe Pairs for mRNA visualization
tanghaibao/allhic
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
loosolab/TOBIAS
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
cpockrandt/genmap
GenMap - Fast and Exact Computation of Genome Mappability
shingocat/lrscaf
TGS scaffolding
medvedevgroup/SibeliaZ
A fast whole-genome aligner based on de Bruijn graphs
malonge/RaGOO
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
PASSIONLab/BELLA
BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper
wtsi-hpag/Scaff10X
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
kuleshov/architect
Scaffolding genomes using synthetic long read clouds
mahulchak/quickmerge
A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
deeptools/HiCExplorer
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
bitly/data_hacks
Command line utilities for data analysis
gmarcais/Jellyfish
A fast multi-threaded k-mer counter
mourisl/Lighter
Fast and memory-efficient sequencing error corrector
josephryan/sowhat
Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)
GregoryFaust/samblaster
samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
Ettwiller/Trawler
Trawler is a integrated pipeline for the analysis of large scale chromatin-immunoprecipitation (ChIP) data and other large scale DNA-RNA datasets.
mermaid-assembler/mermaid
Mermaid Whole Genome Assembler
stamatak/RAxML-Light-1.0.5
stamatak/standard-RAxML
mdrasmus/spimap
Species informed maximum a posteriori gene tree reconstruction
arq5x/bedtools
A powerful toolset for genome arithmetic.
inab/trimal
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0