Mitochondrial Genome Assembly based on low coverage 454 data (Vlog #5)
In todays blog I talk about the mitochondrial genome assembly project I work on together with a bachelor student. We take low coverage sequence data with 90k sequences obtained with a 454 GS Junior system (Roche). As the motochondrial genome of the stonefly Pteronarcys princeps is already available, we use it as a reference genome to assemble our Dinocras cephalotes genome. We use the program blast+ to compare the Pteronacrys genome with our 454 reads. With an R script we export hits that match the MTgenome reference, including the phred quality values for each read. The MT reads of D. cephalotes are assembled and edited with Geneious Pro and regions with sequencing, quality problems or low coverage are resequenced with Sanger sequencing. Feel free to comment if you have questions or feedback = ) http://www.luckylion.de http References: Stewart, JB, Beckenbach, AT (2006). Insect mitochondrial genomics 2: the complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements. Genome, 49, 815--824.
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Mitochondrial Genome Assembly based on low coverage 454 data (Vlog #5) - Video
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