Tk genome project

Tigriopus kingsejongensis genome project

• Abstract

Status of the project

• Tk_genome_v1 : Done and released.
• Tk_genome_v2 : Done and ready to release.

Methods of Tk genome v2

gDNA sequencing

• Library type : Short paired-end (PE), Long read (LR)
• Sequencing data : Illumina Miseq (KOPRI, https://www.kopri.re.kr), HiSeq 2500 (JS.Lee lab, http://tigriopus.skku.edu), PacBio Sequel CLR (JS.Lee lab)

Preprocessing steps for raw reads

• Adapters and low quality reads removal (Trimmomatic, http://www.usadellab.org/cms/?page=trimmomatic)
• Error correction for raw reads (BBtools, JGI https://jgi.doe.gov/data-and-tools/bbtools)
• Contaminated raw reads from prokaryote and fungi (Tool : BBtools, DB : Refgen)

De novo assembly

• Creating contigs (Flye assembler v2.8.1)
• Polishing the draft assembly (Pilon, https://github.com/broadinstitute/pilon)
• Read-based phasing (Whatshap v1)
• Assembly assessment (BUSCO v5, https://busco.ezlab.org/#software)

Gene prediction and annotation

• Consturction of Repeat library (RepeatModeler : http://www.repeatmasker.org/, TEclass : http://www.compgen.uni-muenster.de/tools/teclass)
• Braker2
• Filtering annotated genes (In-house custom script)

Results

Statistics of the draft assembly

[stats table]

Genome browser

• Tk v1.0 : http://210.218.217.114:8085/apollo/1/jbrowse/index.html (Powered by WebApollo & J-browser)
  • Now under maintenance.

Download contents for Tk v1.0 gene information

• Available on the release section
• Tk v2 is in preparation and will be released soon.