Dear all, I am trying to assemble Illumina miseq reads (2x300bp) for my eukaryotic organism. I have the reference genome of an organism of a related species and I would like to use it for my assembly process. I have finished all the basic steps after I received my fastq files such as FTM, adapter removal, trimming/removing low quality reads. Now, as the first step, I have used BWA for aligning my reads to the reference genome (I created the index file before this step). The output that I get is a SAM file. Here my problem begins, I am following this (1) paper. As per the paper, in the next step reads are assigned into blocks according to the alignment. Then superblocks are made, using non-overlapping blocks. But they are not clear about the tools that were used for this process. Has anyone done something similar? Or used a different protocol? Please advice. https://www.pnas.org/content/108/25/10249/
If you are going to spend a lot of time following a paper, are you sure you can't find a more recent one to follow? Do you have dozens of Miseq runs? I don't see how you can assemble anything with 50 million reads unless the genome is really small.
Have you successfully assembled your reads after following this protocol. I am trying to do the same and any help and suggestion would surely gonna help me a lot.
Thank you