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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/MitoHiFi.md
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---
title: Assembling Mitogenomes from PacBio HiFi reads using MitoHiFi
alias: MitoHiFi
aliases:
- MitoHiFi
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: MitoHiFi - Assembling Mitos
---
#BGA23/sessions #MitoHiFi #Assembly #Mitochondrion #PacBio #Pipeline #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/btk-view.md
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---
title: Checking for cobionts in public genomes using BlobToolKit
alias: btk-view
aliases:
- btk-view
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: BTK-view
---
#BGA23/sessions #Workshop #Tools #Cobionts #BlobToolKit #BTK

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/busco.md
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---
title: BUSCO - from QC to gene prediction and phylogenomics
alias: busco
aliases:
- busco
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: BUSCO-QC and Phylogeny
---
#BGA23/sessions #Pipeline #Workshop #BUSCO #Gene_prediction #Phylogenomics #QC

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/cactus.md
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---
title: Aligning whole genomes using Cactus
alias: cactus
aliases:
- cactus
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: Alignments with Cactus
---
#BGA23/sessions #Workshop #Cactus #Alignments #Tools

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/cngbdb.md
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title: Starting a comparative genome study from CNGBdb-datasets, analysis platform, and spatial transcriptomics database
alias: cngbdb
aliases:
- cngbdb
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: Comparative Genomics with CNGBdb
---
#BGA23/sessions #Genomic_study #CNGdb #Transcriptomics

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/earlgrey-te.md
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---
title: Classifying Transposable Elements with Earl Grey TE
alias: earlgrey-te
aliases:
- earlgrey-te
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: Earl Grey TE
---
#BGA23/sessions #Workshop #Earl_Grey_TE #Transposable_elements #TEs #Annotation

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/easel-annotation.md
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---
title: EASEL software for eukaryotic structural and functional genome annotation
alias: easel-annotation
aliases:
- easel-annotation
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: Annotation with EASEL
---
#BGA23/sessions #EASEL #Annotation #Eukaryotes #Pipeline #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/ena-ebi-stands.md
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---
title: ENA Standards and Submission
alias: ena-ebi-stands
aliases:
- ena-ebi-stands
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: ENA Submission
---
#BGA23/sessions #ENA #Submission #Standards #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/enaebi-data.md
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---
title: ENA data retrieval and EMBL-EBI's Biodiversity Portals
alias: enaebi-data
aliases:
- enaebi-data
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: ENA-data retrieval
---
#BGA23/sessions #ENA #Data_download #Web_portal #DTOL_portal #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/ensembl-annotation.md
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---
title: Annotating genomes the Ensembl way
alias: ensembl-annotation
aliases:
- ensembl-annotation
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: Annotation with Ensembl
---
#BGA23/sessions #Annotation #Ensembl #Pipeline #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/genomescope.md
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title: Genome profiling using GenomeScope
alias: genomescope
aliases:
- genomescope
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: GenomeScope
---
#BGA23/sessions #QC #GenomeScope #Kmers #Tools #Workshop

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1 change: 1 addition & 0 deletions content/BGA23/Sessions/gfastar.md
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- gfastar
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: GFastar
---
#BGA23/sessions #Tools #Gfastar #QC #Workshop

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1 change: 1 addition & 0 deletions content/BGA23/Sessions/goat.md
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- goat
date_created: 18-30_04_2024
data_modified: 18_30-04-2024
search_name: GOAT-Querying genomic data
---

#BGA23/sessions #GOAT #Tools #Web_portal #Workshop
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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/hifiasm-telomere.md
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---
title: Scalable telomere-to-telomere assembly with hifiasm
alias: hifiasm-telomere
aliases:
- hifiasm-telomere
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: HiFiasm on T2T assemblies
---
#BGA23/sessions #Assembly #HiFiasm #Tools #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/manual-curation.md
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title: Introduction to Manual Curation - HiC and JBrowse
alias: manual-curation
aliases:
- manual-curation
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: Genomic Curation
---
#BGA23/sessions #Process #Curation #Reads-to-Reference/3 #Pretext #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/merqury.md
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title: Assess genome assemblies with Merqury
alias: merqury
aliases:
- merqury
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: Merqury genome assessment
---
#BGA23/sessions #Merqury #Kmers #Tools #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/ncbi-cgv.md
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---
title: Compare whole genome assembly alignments using NCBI’s Comparative Genome Viewer (CGV)
alias: ncbi-cgv
aliases:
- ncbi-cgv
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: CGV and whole genome alignments
---
#BGA23/sessions #Visualisation #NCBI #QC #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/ncbidatasets.md
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title: Searching and Downloading Genome Data using NCBI Datasets
alias: ncbidatasets
aliases:
- ncbidatasets
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: NCBI Datasets
---
#BGA23/sessions #Data_download #NCBI_datasets #Workshop

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1 change: 1 addition & 0 deletions content/BGA23/Sessions/nextflow-genomics.md
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- nextflow-genomics
date_created: 18-30_04_2024
data_modified: 18_30-04-2024
search_name: Nextflow in Genomics
---

#BGA23/sessions #Pipeline #Nextflow #NF-Core #Workshop
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1 change: 1 addition & 0 deletions content/BGA23/Sessions/oma-omark.md
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- oma-omark
date_created: 18-30_04_2024
data_modified: 18_30-04-2024
search_name: OMA and OMArk
---

#BGA23/sessions #Orthology #Homology #OMA #OMArk #Annotation #QC #Workshop
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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/pangenome.md
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---
title: Pangenome Assembly and Assessment using Minigraph and Bandage
alias: pangenome
aliases:
- pangenome
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: Minigraph and Bandage for Pangenomes
---
#BGA23/sessions #Assessment #Bandage #Minigraph #Workshop

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1 change: 1 addition & 0 deletions content/BGA23/Sessions/smudgeplot.md
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- smudgeplot
date_created: 18-30_04_2024
data_modified: 18_30-04-2024
search_name: Smudgeplot-Kmers and Ploidy
---

#BGA23/sessions #Kmers #Smudgeplot #Workshop
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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/treeval-curation.md
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---
title: The Treeval pipeline Generating evidence for manual curation
alias: treeval-curation
aliases:
- treeval-curation
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: TreeVal Pipeline
---
#BGA23/sessions #Nextflow #Pipeline #TreeVal #Visualisation #Reads-to-Reference/2 #Workshop

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4 changes: 3 additions & 1 deletion content/BGA23/Sessions/vgpgalaxy.md
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---
title: Assembling Genomes with the VGP-Galaxy Pipeline
alias: vgpgalaxy
aliases:
- vgpgalaxy
date_created: 18_30-04-2024
data_modified: 18_30-04-2024
search_name: VGP-Galaxy Pipeline
---
#BGA23/sessions #Galaxy #VGP #Pipeline #Assembly #Reads-to-Reference/1 #Workshop

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26 changes: 19 additions & 7 deletions content/index.md
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title: Welcome to The Biodiversity Genomics Academy homepage!
created: 27/02/2024
---
![[BGA_final.png]]
<h1 align="center"> Join us October 1st - 26th </h1>

>[!info]
>This website is still in development and will not be complete for sometime. If there is anything wrong or you need something specific then please contact me, Damon (this years organiser!), at `damon[@]thebgacademy.org`.
>This website is still in development and will not be complete for sometime. If there is anything wrong or you need something specific then please contact me Damon (this years organiser!) at
> --> `damon[@]thebgacademy.org` <--
Here we are planning the future of BGA, a series of **free, open to all, online-only, short, interactive** sessions on how to use the bioinformatics tools and approaches that underpin the [Earth Biogenome Project (EBP)](https://earthbiogenome.org) and the field as a whole.
Welcome to BGA!!!

BGA is a series of **free, open to all, online-only, short and interactive** sessions on how to use the bioinformatics tools and approaches that underpin the [Earth BioGenome Project](https://www.earthbiogenome.org/) and the field as a whole.

We are actively planning BGA24 right now and we want it bigger and better than last year!

To register your interest for the year here's a form you can fill in! Once we have our session time table locked in, I'll send out a new questionnaire to ask which ones you'd like to attend. This will be so we can gage interest and may run some repeat sessions!

<div data-fillout-id="s3AzWt1p8Nus" data-fillout-embed-type="popup" data-fillout-button-text="Register your interest!" data-fillout-button-color="#00D084" data-fillout-button-size="medium" data-fillout-inherit-parameters></div>
<div align="center" data-fillout-id="s3AzWt1p8Nus" data-fillout-embed-type="popup" data-fillout-button-text="Register your interest!" data-fillout-button-color="#00D084" data-fillout-button-size="medium" data-fillout-inherit-parameters></div>

<script src="https://server.fillout.com/embed/v1/"></script>

If you already know you want to be a session leader then this is the form for you:

<div data-fillout-id="k15yEJyr3xus" data-fillout-embed-type="popup" data-fillout-button-text="Session Leader Form" data-fillout-button-color="#9900EF" data-fillout-button-size="medium" data-fillout-inherit-parameters></div>
<div align="center" data-fillout-id="k15yEJyr3xus" data-fillout-embed-type="popup" data-fillout-button-text="Session Leader Form" data-fillout-button-color="#9900EF" data-fillout-button-size="medium" data-fillout-inherit-parameters></div>

<script src="https://server.fillout.com/embed/v1/"></script>

Find out more about this years BGA --> [[BGA24|HERE]] <--
<h3 align="center"> Find out more about this years BGA [[BGA24|HERE]] </h3>

## What is The BGA?

BGA was started with [[BGA23]], found here on the [original site](https://bga23.org/), however, going forward this will be the go to site for all things BGA! All Workshops, talks and guides will be directed to and from here to act as a central point in the eduction of bioinformaticians worldwide!

BGA23 was the test bed, the team (the one man team at the time, [[Sujai Kumar]]) aimed for 20 workshops and ~20 participants each. This culminated in >40 workshops with >1500 attendees. Simply amazing!

## FAQs
Frequently asked questions can be found here: [[FAQs]]
### [[FAQs | BGA FAQs!]]

# What about BG?

BGA works hand in hand with the BioDiversity Genomics conference (28th October - 1st November).

At BG you can join thousands of researchers worldwide and hear all the latest findings and ideas as we strive to complete the goals of the [Earth BioGenome Project](https://www.earthbiogenome.org/): “sequencing life for the future of life”. 

The meeting will be a mix of sessions with invited talks, including keynote presentations, and open sessions proposed by researchers around the world. There will be a focus on regional initiatives and on the global drive to ensure equity and justice in biodiversity sequencing.

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