Question: How to find Bloom filter parameter for Abyss 2
0
gravatar for Ric
3.0 years ago by
Ric280
Australia
Ric280 wrote:

Hi, Abyss 2 introduces a new Bloom filter assembly mode that enables large genome assemblies with minimal memory. Bloom filter assembly mode is enabled by adding three 'abyss-pe' parameters B (Bloom filter size), H (number of Bloom filter hash functions), and kc (minimum k-mer count threshold).

How do I determine these parameters?

Thank you in advance.

Mic

bloom filter assembly genome • 1.2k views
ADD COMMENTlink written 3.0 years ago by Ric280

Probably this post might help -

abyss/konnector2 : Usage Scenario

The kmer count depends on your coverage too, I usually calculate that with bbnorm. For bloom filter size, Ben suggests 40G for 80X human data, so depends on how much data you have now. I have no idea about the number of hash functions. How about running at different values and check how well the FPR decreases from the log file. Not optimal, but practical I guess.

ADD REPLYlink written 3.0 years ago by Rohit1.4k
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