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gecko

The official repository of the gecko gene cluster software

gemma

Genome-wide Efficient Mixed Model Association

gencore

Generate consensus reads to reduce sequencing noises and remove duplications

gene_prediction

Gene prediction pipeline. FROM LZU.

genefuse

Gene fusion detection and visualization

genodup-pipeline

This python script can be used to detect Whole-genome duplication (WGD) with the dS based method.

genome-annotation-pipeline

Genome annotation

genome-rearrangements

genome_annot

genome annotation

genome_annotation

The genome annotation service provides automated gene annotation based on the RAST system. This deploys both client and service components.

genomealign

genomealignmenttools

Tools for improving the sensitivity and specificity of genome alignments

genomeannotation

Best practices and workflow for genome annotation

genomeannotator

Pipeline for the identification of (coding) gene structures in draft genomes.

genomemining

Methodologies for genome mining and annotation

genomeplot

Plot bedfiles over the entire genome with chromIdeoBands

genomeplots

Plot genomic data in high definition

genomescope

Fast genome analysis from unassembled short reads

genomethreader

GenomeThreader gene prediction software.

genomeview

An extensible python-based genomics visualization engine

genomic_tools

Genomic related tools

gephi

Gephi - The Open Graph Viz Platform

gephi-plugins

Repository for Gephi Plugins maintained by the team. Each plugin has it's branch.

gephi-toolkit

Gephi Toolkit - https://gephi.org/toolkit

geta

GETA is an automatic genome-wide annotation tool (GWAT) with improved accuracy and gene integrity for eukaryotes

gfa-spec

Graphical Fragment Assembly (GFA) Format Specification

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

gfftools

Perl scripts for working with the GFF format

ggcoverage

Visualize and annotate genomic coverage with ggplot2