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.