I wrote a "script" to pull out reads from a huge fastq file in an iterative manner, by finding homology to the previous sequence.
It should be relatively easy to overlap them and assemble the gene, however traditional assemblers like SPAdes fail due to obviously low coverage.
I am hesitant to just feed it more faked reads, when I know I have all the data necessary to just overlap them into a single sequence.
The reads are set up like this:
GATCAAACATC AACATCAGTTAG TCAGTTAG TAGAGGATAGC
What kind of assembler is out there where I can feed it this kind of terribly-formatted data?