I am trying to assemble tandemly repeated sequences and I am looking for an assembler that has an option “only use paired-end reads during assembly”, or something like this.
Does anyone have any suggestions?
I am not answering your question directly since many assemblers will use paired-end reads. Since PE technology is available with short reads I assume that is what you have.
Just having paired end reads will not be enough to assemble tandem repeats especially depending on the length of the individual repeat and their number. You may need data from a long read technology like nanopore/PacBio to be able to traverse the repeats reliably.
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