leahkemp / guinea_pore_c

Analysis documentation for part of the reference genome assembly of the humble guinea pig. Oxford Nanopore Technologies (ONT) pore-c data.

Guinea pore-c

General info

This relates to the reference genome assembly of the humble guinea pig (Cavia porcellus) undertaken by the human genomics group at ESR (yes the irony I know). Building a better reference genome assembly for the wee guinea pig is an attempt to improve the genetic analyses in studies on premature birth using the guinea pig as a model organism. Oxford Nanopore Technologies (ONT) pore-c data.

Raw data location

• The raw data for this project is stored/backed up at /mnt/cavia_porcellus/genome_sequencing/guinea_pore_c/ on ESR's research network (Leviathan)

Analysis location

• This analysis was for the most part carried out at /NGS/scratch/KSCBIOM/HumanGenomics/guinea_pore_c/ on ESR's production network
• A minimal version of the analyses were stored/backed up at /NGS/clinicalgenomics/archive/2022/results/guinea_pore_c/ on ESR's production network

Analysis workflow for reproducing this analysis

• 01 - Assumptions
• 02 - Basecallling
• 03 - Initial QC
• 04 - Pore-c snakemake pipeline run
• 05 - Look at outputs
• 06 - Data visualisation
• 07 - Cleanup

Access

• The github repository for this project is public
• For other general queries about this project beyond the bioinformatics, contact the current (2022) representatives of the ESR genomics group, Donia Macartney-Coxson ([e-mail]) and/or Joep de Ligt ([e-mail])

Github repository

Find the github repository for this project at: https://github.com/leahkemp/guinea_pore_c

Results webpage

Find the rendered webpage of results for this project at: https://leahkemp.github.io/guinea_pore_c