Best way to assemble a genome with a reference

Question

[genseq]

What is the most canonical way to assemble a bacterial genome (with a reference) from Illumina paired-end reads?

There is a scheme I want to follow: make contigs with SPAdes -> align those with bowtie2 to reference -> whats next?

[Joe]

You wouldnt assemble with spades if you want to do reference-guided as its specifically a de novo assembler. You'd use a proper reference guided assembler (unless spades has introduced an optional flag/alternative mode I'm not aware of).

The only one I know off the top of my head is MIRA assembler.

[genseq]

Thanks.

What about bowtie2/bwa alignment with further consensus calllig? Is it reliable?

[Joe]

You are asking about alignment and assembly. These are two different things.

Answer 1

[rohitsatyam102]

I think you must check out this paper. The Pipeline presented is what I think you require for reference guided genome assembly of the bacterial genome.