Hey RG community,

I'm wondering if anyone knows of a good genome assembler software (and the code needed) to assemble NGS data (Illumina/ON/PacBio) based on a single sequence, building from this sequence, but ignoring any other possible contigs, to make the assembly fast and targeted?

Essentially, I want to give the assembler a single sequence (a gene perhaps) and ask the software to simply build out from what I provide to give me the longest possible contig., while ignoring any reads that don't associate.

The reason behind this, is that we have some huge datasets that would take weeks to assemble in their entirety. If I can get an assembler to focus on just one sequence input and build from that, and ignore the rest of the data, it might give me a faster way to pull out specific contigs of interest without completing a total assembly.

FYI: I do not have the full sequence I am looking for, only a short read that I want to build out from to create a contig. So mapping isn't quite the way to get the job done, unless I wanted to very slowly build on the edges. I'd like a quick way, if possible.

Thanks for your help,

Jamie