Megraft
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Application data |
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| Created by | Bengtsson J |
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| Biological application domain(s) | Metagenomics, Phylogenetics, Sequence analysis, Community analysis, Rarefaction |
| Principal bioinformatics method(s) | Hidden Markov Model, Sequence analysis |
| Technology | 454, ABI SOLiD, Illumina, Ion Torrent, Sanger |
| Maintained? | Maybe |
Summary: Megraft is a software tool to graft ribosomal small subunit (16S/18S) fragments from metagenomes onto full-length SSU sequences, enabling accurate diversity estimates from fragmentary and non-overlapping sequence data.
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Description
Megraft is a software tool to graft ribosomal small subunit (16S/18S) fragments onto full-length SSU sequences. Megraft is built upon the notion that when examining the depth of a community sequencing effort, researchers often use rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in a metagenome. However, the SSU sequences in metagenomic libraries generally are present as fragmentary, non-overlapping entries, which poses a great problem for this kind of analysis. Megraft aims to remedy this problem by grafting the input SSU fragments from the metagenome (obtained by e.g. Metaxa) onto full-length SSU sequences. The software also uses a variability model which accounts for observed and unobserved variability. This way, Megraft enables accurate assessment of species richness and sequencing depth in metagenomic datasets.
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