Rice is one of the most important crops for human. The third-generation sequencing (TGS, also called long-read sequencing, LRS) helps us assemble more high-quality genomes and construct more complete pan-genomes. Here are codes of the article "Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes".
The main pipelines are as following and the main self-writen scripts are in "scripts" directory.
The pipeline of preprocessing, assembling, polishing and scaffolding from raw long/short reads to assemblies.
The pipeline of SV calling, filtering and merging from long reads to SVs.
The pipeline of filling gaps in Nipponbare genomes with corrected reads and assembled contigs.
The pipeline of constructing pan-genomes from genomes.