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Table 1 Details of steps implemented in Minia

From: Space-efficient and exact de Bruijn graph representation based on a Bloom filter

Step

Time (h)

Memory (Gb)

k-mer counting

11.1

Constant (set to 4.0)

Enumerating positive extensions

2.8

3.6 (Bloom filter)

Constructing cFP

2.9

Constant (set to 4.0)

Assembly

6.4

5.7 (Bloom f.+ cFP

  

+ mark. struct.)

Overall

23.2

5.7

  1. Details of steps implemented in Minia, with wall-clock time and memory usage for the human genome assembly. For constant-memory steps, memory usage was automatically set to an estimation of the final memory size. In all steps, only one CPU core was used.
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Algorithms for Molecular Biology

ISSN: 1748-7188