芥菜的组装

[anneng]

https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13492
A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes high molecular weight DNA isolated from B. juncea variety Varuna was subjected to SMRT sequencing on the PacBio RSII platform. A total of 9 735 857 reads, with an N50 value of ~15.5 kb, were obtained—providing ~100× coverage of the genome (Table S1). The reads were assembled into 1253 contigs with an N50 value of ~5.7 Mb using Canu assembler (Table 1).

Sequences generated from the three PE libraries of B. nigra were assembled into contigs with MaSuRcA software (Zimin et al., 2013). Illumina PE reads were mapped on the raw Nanopore reads using BWA mem; 1 442 476 error corrected Nanopore reads were generated using the Pilon program (Walker et al., 2014). Scaffolding of the MaSuRcA based contigs with the error corrected Nanopore sequence data was carried out with SSPACE-LongRead.pl script (Boetzer et al., 2011), which generated 29 808 scaffolds with an N50 value of 19 834. Further, three rounds of scaffolding were carried out using the 2 kb, 6 kb and 10 kb MP library sequence data sets using SSPACE-STANDARD-3.0.pl script (Boetzer et al., 2011).