Best way to assemble a genome with a reference
1
0
Entering edit mode
3.6 years ago
genseq • 0

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?

assembly genome • 1.2k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thanks.

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
3.6 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1675 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6