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3d-genome-builder

3DGB is a workflow to build 3D models of genomes from HiC data

aaftf

Automatic Assembly For The Fungi

abshare.github.io

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anchorwave

sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

annosine

SINE annotation tool for plant genomes

annotationpipeline-evm_based-dclab

Cantù Lab @ UC Davis - Annotation pipeline - EVM based

awesome-bioinformatics-cn

生物信息学软件，资源和工具库的精选列表

awesome-pangenomes

A list of software for pangenomics

biocode

Bioinformatics code libraries and scripts

cas-offinder

An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.

crisprdesign

Comprehensive design of CRISPR gRNAs for nucleases and base editors

custardpy

A docker image for 3D genome analysis

dap_learning

Deep learning motif discovery using DAP-seq data

deepcnv

DeepCNV: A Deep Learning Approach for Authenticating Copy Number Variants

drompaplus

ChIP-seq pipeline tool for quality check, normalization, statistical analysis, and visualization of multiple ChIP-seq samples.

edta

Extensive de-novo TE Annotator

effectorp-3.0

Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes

fanc

FAN-C: Framework for the ANalysis of C-like data

free

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gaep

A genome assembly assessment pipeline.

genion

gene fusion

genome-annotation-pipeline

Genome annotation pipeline

ginger

graffite

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

great_3d

A tool for the analysis and visualisation of 3d genome structure, epigenetics and gene expression.

griffindetector

To find fusion genes by protein sequences at genome level from several closely related species

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

gwas

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

gwastutorial

GWAS Tutorial for Beginners

haplotype_genome_assembly

Genome haplotype assembly and assessment method