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Table 4 Memory consumption to implement index structure (MB).

From: Short read DNA fragment anchoring algorithm

Index name

First-level

Second-level

Total

EMBF-12 bps

28.24

247

275.24

EMBF-16 bps

49

99

148

BTree-11 bps

176

397

573

BTree-16 bps

342

397

739

BLAT

-

-

60

SOAP

-

-

562

  1. We divide the memory consumption for EMBF and BTree to two separate parts, the first part is used to build a hash map for EMBF and a traversal query tree for BTree; the second part is used to store positional information for EMBF and remaining sequences for BTree. The -xbps suffix in index name column indicates that the algorithm using seed with length of x bps.