Genotype specific transcriptome assemblies - Fasta files

Genotype-specific de novo transcriptome assemblies from sugarcane RNASeq public datasets.RAW RNASeq reads (paired-end and strand-specific) were downloaded from SRA's NCBI, cleaned with BBDuk and putative contaminant reads removed with ContFree-NGS. Clean reads were assembled into transcripts with Trinity using two kmers, 25 and 31. The two assemblies were merged using CD-HIT-EST at 100% identity and keeping strand orientation.

本研究从NCBI的SRA数据库中下载了甘蔗RNASeq公共数据集的原始RNASeq reads（包括配对端测序和定向测序），使用BBDuk进行清洗，并通过ContFree-NGS软件移除了潜在的污染读段。经过清洗的reads利用Trinity组装成转录本，采用了两个kmer长度，分别为25和31。随后，通过CD-HIT-EST在100%的相似度下进行组装合并，同时保留了定向信息。