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agbiodata_gff3_recommendation

The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome discussion of these recommendations from the larger community.

agla_gb_supp-scripts

This repository contains scripts used for various sections of the paper "Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface".

annothelper

apollo

Customized version of Apollo, which is a genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

assembly_metrics_toolkit

Simple toolkit for assembly metrics calculation.

assembly_metrics_visualization

Visualization based on the calculation result of Assembly Metrics Toolkit. (https://nal-i5k.github.io/Assembly_Metrics_Visualization/)

automatic_fillin_prototype

bam_to_bigwig

Convert your alignment files in BAM format into coverage files in bigWig format

colorbytype

A JBrowse plugin to color the features according the feature type

content_onboarding_scripts

Ancillary scripts for onboarding content at the i5k Workspace.

coordinates_conversion

Conversion programs that use the output from fasta_diff.py to convert coordinates and IDs in different format files.

customize_refseq

django-blast

NCBI-BLAST web service with python backend and HTML5 frontend.

gene_jbrowse_field

Create JBrowse field on Tripal 3 Gene Pages

general_issues

for issues and discussions not tied to a specific repository

genomics-vm

Setup your development environment for genomics applications easily by setting up a Virtualbox VM through Vagrant.

genomics-workspace

Django website project for common sequence search tools.

genomics-workspace_docker

genomics_workspace_tests

Production tests for genomics-workspace.

gff3toolkit

Python programs for processing GFF3 files

github_stat

Generate statistics report (commit/insertion/deletion) of your github repos

i5k_analysis

drupal Features module for analysis bundle

i5k_custom_fields

Provides custom fields for i5k Tripal sites.

i5k_custom_tripal

i5knal_ogs

NOTE: This repo is no longer maintained, please refer to https://github.com/NAL-i5K/GFF3toolkit/. This project is to develop python tools for generating official gene set (OGS) by integrating manually curated and predicted gene annotations (GFF3 format). There are two phases involved: (1) QC phase and (2) Merge phase.

image_permission_form

This is the blank image permission form needed when submitting projects to the i5k Workspace@NAL.

jbrowse

Customized version of jbrowse used for NAL-i5k

jbrowse-plugin-linkout

jbrowse_track_configs

This is a repository to collect our JBrowse and Apollo track configuration files.

nal-genomics-workspace

NAL specific customizations to the genomics workspace application