# Finding simple sequence from reads with significant overlap

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?

By default it looks for overlap regions that have a coverage of 3 reads when joining (option -c), but I assume that could be reduced down to 2 reads, as in your example (which has a minimum overlapping coverage of 2).