Sealer/Konnector loading a bloom filter from a file

Question

[jshelton]

Hello,

I see parameters to load bloom filters from a file for Sealer and Konnector. I don't see any parameter to save bloom filter to a file for either program. What commands are used create/save a bloom filter to a file in case it is needed for a second run?

I also posted this on the google group (before I saw the request to post questions here).

Thanks so much,
Jennifer M Shelton

Answer 1

[benv]

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.