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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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Help: Jellyfish Configurations #106

Closed taranglute closed 6 years ago

taranglute commented 6 years ago

Hi

We are working on analysis of Bioinformatics tools (related to Kmer counting) and Jellyfish 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: Hash Table/ Hashing,Bloom filter Approach: Multi-threaded using compare and swap operation The limit of k-size : less than 500 (NOT SURE) Supports online k-mer frequency retrieval : Yes Supports compressed file processing : No

Query Which approach Jellyfish use for kmer counting

  1. Disk based
  2. In memory

Thanks Tarang

gmarcais commented 6 years ago

limit of k-size: no real limit. compressed file processing: yes in the later version. approach: mostly in memory. Uses disk if memory fills up