Improved error handling

Check return codes from KMC and SPAdes.
Account for FASTQ files without slashes at the end.

Improved contiguation of final sequences

A second round of filtering and assembly has been added.
There is also better support for filtering out noise and low coverage contigs.

Cleanup SPAdes output and expand documentation

Merge pull request #2 from andrewjpage/master

Output scaffolds, cleanup SPAdes output, expand documentation

Allow for intersection of trait kmers

Merge pull request #1 from andrewjpage/master

Allow intersection

Initial version

v0.01

spades doesnt support python 3.6 yet