search

uni-halle / gerbil

A fast and memory-efficient k-mer counter with GPU-support
MIT License
34 stars 14 forks source link

Help: Gerbil Configuration #7

Open taranglute opened 6 years ago

taranglute commented 6 years ago

Hi

We are working on analysis of Bioinformatics tools (related to Kmer counting) and Gerbil is one of them. We have gone through readme file and it is very helpful. As we are doing analysis so we want to be very sure about details. It would be great if you help us validating below details.

Data structure and Sorting Algo: Array/Hashing

Approach: Two disk based, modified minimum sub-string partitioning (Signature), GPU implementation

The limit of k-size : less than 521 Supports online k-mer frequency retrieval : No Supports compressed file processing : Yes

Thanks Tarang

srechner commented 6 years ago

Hi,

thanks for your interest in our work. It seems all of your details are correct.

Steffen