- De novo assembly using the short-read sequencing technology
- Library type : Short paired-end (PE), Long mated-pair (MP)
- Sequencing methods : Illumina Miseq, HiSeq 2500
- Adapters and low quality reads removal (Trimmomatic, http://www.usadellab.org/cms/?page=trimmomatic)
- Nextera adapters removal (Skewer, https://github.com/relipmoc/skewer)
- Error correction for raw reads (BBtools, JGI https://jgi.doe.gov/data-and-tools/bbtools)
- Duplicated reads removal (FastUniq, https://sourceforge.net/projects/fastuniq)
- Contaminated raw reads from prokaryote and fungi (Tool : BBtools, DB : Refgen)
- Creating contigs (Platanus, http://platanus.bio.titech.ac.jp/)
- Reconstruction of high polymorphic region (HaploMerger2, https://github.com/mapleforest/HaploMerger2)
- Polishing the draft assembly (Pilon, https://github.com/broadinstitute/pilon)
- Assembly assessment (BUSCO v3, https://busco.ezlab.org/#software)
- Braker1 (http://exon.gatech.edu/braker1.html)
- Maker pipeline with BUSCO, SNAP, AUGUSTUS, GeneMark
- Consturction of Repeat library (RepeatModeler : http://www.repeatmasker.org/, TEclass : http://www.compgen.uni-muenster.de/tools/teclass)
- Filtering annotated genes (In-house custom script)
- Manual annotation (Web-apollo, http://genomearchitect.org)
| Tk v1 assembly | |
|---|---|
| Scaffolds No. | 1,066 |
| Total length (bp) | 196,471,422 |
| N50 (bp) | 818,552 |
| Max contig length (bp) | 4,767,029 |
| Gap | 2.91% |
| GC contents | 45.87% |