Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1

About the assembly

The TM-1 assembly was conducted using a Canu-based pipeline (Koren, S. et al. 2017) with the following procedures: longer seed reads were selected with the settings genomeSize = 600000000 and corOutCoverage = 35; raw reads overlapping was detected through a high sensitive overlapper MHAP (mhap-2.1.2, option corMhapSensitivity = low/normal/high), and an error correction was performed through Falcon sense method (option correctedErrorRate = 0.025); error-corrected reads were trimmed of unsupported bases and hairpin adapters in order to reach their longest supporting range with the default parameters, and then the draft assembly was generated using the top 80% longest trimmed reads. The raw Illumina reads were filtered as mentioned in the Illumina sequencing section. Finally, the clean reads from the same sequencing individuals were integrated to correct the SNPs and InDels in the draft assemblies using Pilon v1.22 (Walker, B. J. et al., 2014) with the parameters -mindepth 10 –changes –threads 4 –fix bases.

Publication

Yang, et al., Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nature Communicationsvolume 10, Article number: 2989 (2019).