For future reference, here was my response on the ABySS Google Group:

Hi Jennifer,

There is a separate program for building Bloom filters called abyss-bloom. You can use the Bloom filter files generated by abyss-bloom with both Konnector and Sealer.

Here is an example:

$ abyss-bloom build -k50 -vv -q15 -j10 -b40G -l2 output.bloom reads.fq

Options:

* -k is k-mer size

* -vv is verbose logging

* -q15 means quality-trim read tails until first base with phred score >= 15

* -b40G means make a 40GB Bloom filter

* -l2 means make a 2-level cascading Bloom filter (to remove error k-mers)

* `output.bloom` is the generated Bloom filter file

* `reads.fq` are the input sequencing reads.