Question: Sealer/Konnector loading a bloom filter from a file
0
gravatar for jshelton
3.3 years ago by
jshelton0
jshelton0 wrote:

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

abyss assembly • 881 views
ADD COMMENTlink modified 3.3 years ago by benv710 • written 3.3 years ago by jshelton0
0
gravatar for benv
3.3 years ago by
benv710
Canada
benv710 wrote:

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

--- BEGIN QUOTE ---

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.

--- END QUOTE ---

ADD COMMENTlink written 3.3 years ago by benv710
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