Unmapped reads from cattle RNAseq data: A source for missing and misassembled sequences in the reference assemblies and for detection of pathogens in the host

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• 作者：Tahir Usman^a ; ^b ; Frieder Hadlich^a ; Wiebke Demasius^a ; Rosemarie Weikard^a ; Christa Kü ; hn^a ; ^c ; ^{kuehn@fbn-dummerstorf.de} ;
• 关键词：Unmapped reads ; Next generation sequencing ; RNAseq ; Bioinformatics
• 刊名：Genomics
• 出版年：2017
• 出版时间：January 2017
• 年：2017
• 卷：109
• 期：1
• 页码：36-42
• 全文大小：752 K
• 卷排序：109

文摘

Unmapped reads from transcriptome sequencing data can provide information regarding the presence of microorganisms in mammalian samples. We found that several parasite and virus genome reference assemblies in NCBI were contaminated with bovine DNA. We confirmed recombination of bovine genomic DNA into BVD virus strains. De novo assembled contigs of unknown unmapped reads demonstrated incomplete bovine reference genome assemblies.