Question: How to find Bloom filter parameter for Abyss 2
gravatar for Ric
2.6 years ago by
Ric190 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.


bloom filter assembly genome • 1.1k views
ADD COMMENTlink written 2.6 years ago by Ric190

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 2.5 years ago by Rohit1.3k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 829 users visited in the last hour