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3d-dna

3D de novo assembly (3D DNA) pipeline

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

augustus

Genome annotation with AUGUSTUS

bat1k

Perl scripts used in Bat1K annotation for adding splice informative isoforms

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

cesar2.0

genomescope

Fast genome analysis from unassembled short reads

gsalign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hicplotter

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

hirise_july2015_gr

test repository

juicebox

Visualization and analysis software for Hi-C data -

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

lachesis

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

marginpolish

MarginPolish: Graph based assembly polishing

mouse_methylation

msap

The package msap provides a easy way to analyse MSAP (Methylation-Sensible Amplified Polymorphism) data in order to asses epigenetic and genetic differences between groups of samples.

nextdenovo

Fast and accurate de novo assembler for third generation sequencing (TGS) reads

nextpolish

Fast and accurately polish the genome generated by noisy long reads.

quast

Genome assembly evaluation tool

salsa

SALSA: A tool to scaffold long read assemblies with Hi-C data

shang_smart_seq

shasta

De novo assembly from Oxford Nanopore reads.

smartdenovo

Ultra-fast de novo assembler using long noisy reads

toga

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.