demo_GAP

Just some examples to have better understanding of the GAP project, under GSOC'25.😊

Note- This is just for better understanding of the possible approaches, and in no way reflects the actual approaches that will be implemented.

Overall Flowchart -

References

• Nextflow - https://www.nextflow.io/
• nf core - https://nf-co.re/docs/
• Sanger-tol - https://github.com/sanger-tol
• GAP database - https://gap.cog.sanger.ac.uk/
• Project Board - https://github.com/orgs/sanger-tol/projects/3/views/23
• All pipelines - https://pipelines.tol.sanger.ac.uk/genome_after_party
• Genome Assembly - https://github.com/sanger-tol/genomeassembly
• fasta_windows - https://github.com/tolkit/fasta_windows
• All file formats info - https://genome.ucsc.edu/FAQ/FAQformat.html
• Sanger Guidelines - https://pipelines.tol.sanger.ac.uk/docs/contributing/review_checklist
• Bedtools - https://bedtools.readthedocs.io/en/latest/
• bedtobigBed - https://www.encodeproject.org/software/bedToBigBed/
• Some Genome assemblies datasets I found online - NCBI - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/
• View Done Datasets

Sequence compostion -

https://github.com/sanger-tol/sequencecomposition

Simple repet annotation tools -

• refer GDA pipeline - https://github.com/sanger-tol/gda
• Telomeric annotations -
  • treeval - https://github.com/sanger-tol/treeval
  • telomere finder - https://pipelines.tol.sanger.ac.uk/treeval/1.2.2/output#telo-finder

Advanced repeat annotation tools -

• TRASH - https://github.com/vlothec/TRASH

• Earlgrey - https://github.com/TobyBaril/EarlGrey

  • more info - https://academic.oup.com/mbe/article/41/4/msae068/7635926?login=true

• Pantera - https://github.com/piosierra/pantera

• ModDotPlot - https://github.com/marbl/ModDotPlot

Mappability tracks -

• Genmap - https://nf-co.re/modules/genmap_map/

Variant calling/composition-

Variant Calling - https://github.com/sanger-tol/variantcalling/tree/main

• deepvariant - https://github.com/google/deepvariant
• PSMC - https://github.com/lh3/psmc
• RaisD - https://github.com/alachins/raisd
• SnpEff - https://github.com/pcingola/SnpEff
  • Info on SnpEff and SnpSift: https://pcingola.github.io/SnpEff/snpeff/introduction/
• Samtools RoH - https://samtools.github.io/bcftools/howtos/roh-calling.html

Additional Clarifications -

• Population Genomics
• Variant calling on long read data