We have sequenced plant through whole-genome short gun sequencing approach with illumina paired-end reads. I am thinking to extract mitochondiral reads by mapping against available mitochondrial genomes in NCBI. Two options comes to my mind
1. Denovo genome assembly using velvet and blast against genbank mitochondrial genomes to extract mitochondrial reads and proceed for denovo mitochondrial genome assembly.
2. To align the reads to each mitochondiral genome using tophat or any other aligner like bowtie or bwa and extract mitochondiral related reads and then proceed for denovo mitochondrial genome assembly
I like the option two, because we can extract without denovo genome assembly. But the daunting task will be mapping raw reads and extracting mapped reads for each genome. Are there any script available already to extract mapped reads?
Which method is the best one you think?
1. Denovo genome assembly using velvet and blast against genbank mitochondrial genomes to extract mitochondrial reads and proceed for denovo mitochondrial genome assembly.
2. To align the reads to each mitochondiral genome using tophat or any other aligner like bowtie or bwa and extract mitochondiral related reads and then proceed for denovo mitochondrial genome assembly
I like the option two, because we can extract without denovo genome assembly. But the daunting task will be mapping raw reads and extracting mapped reads for each genome. Are there any script available already to extract mapped reads?
Which method is the best one you think?
Comment