I have been given the task of assembling a 'new' Ecoli genome and analysing the genes present etc.
The Ecoli is a new strain, and has been taken and run on a Nextseq 500 in high-output mode with 150bp paired end reads. The 'raw' files that I have is the forward and reverse reads.
I have initially QC checked the 'raw' files, and subsequently run them through trim galore and checked the QC after that.
For the next step, I now need to assemble my genome. I have been told that SPades will run a 'de novo' assembly for me, and then put that assembly into Prokka for Gene annotation.
Is this the best way to assemble the genome and annotate it? Or should I use another method? I am thinking that I should use a 'mapping' technique to assemble the genome using the Ecoli O157:H7 genome as a reference, but I have no idea how to do this. I would say that I am at an intermediate level with unix, but by no means am I a bioinformatician. Some help and guidance would be greatly appreciated!