What are some Prokayotic assembly tools that use a reference fasta
I have short read sequences of several isolates that I want to assemble into contigs. I know what these isolates are so I can use a reference genome to improve the assembly process.
Trouble is I don't know what assembler to use, I typically work with metagenomes so use tools like spades and megahit, although to my understanding they don't use a reference file.
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