Best way to assemble a genome with a reference
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?
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rohitsatyam102
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genseq •
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genseq •
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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.
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You wouldnt assemble with
spadesif 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.Thanks.
What about bowtie2/bwa alignment with further consensus calllig? Is it reliable?
You are asking about alignment and assembly. These are two different things.