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Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.

Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package - Megraft - that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.

Pubmed ID: 22824070


  • Bengtsson J
  • Hartmann M
  • Unterseher M
  • Vaishampayan P
  • Abarenkov K
  • Durso L
  • Bik EM
  • Garey JR
  • Eriksson KM
  • Nilsson RH


Research in microbiology

Publication Data

July 3, 2012

Associated Grants


Mesh Terms

  • Computational Biology
  • DNA, Ribosomal
  • Environmental Microbiology
  • Metagenome
  • Metagenomics
  • RNA, Ribosomal, 16S
  • RNA, Ribosomal, 18S
  • Software