Extensions

Full name SMRUCC.genomics.Analysis.Metagenome.greengenes.Extensions Assembly SMRUCC.genomics.Analysis.Metagenome Members 2

01 Syntax

SMRUCC.genomics.Analysis.Metagenome.greengenes.Extensions

02 Methods

Name	Overloads	Summary
OTUgreengenesTaxonomy	1	Create taxonomy assignment result and OTU aboundance data via gast algorithm.
TreeAssign	1

03 Members

method OTUgreengenesTaxonomy #

OTUgreengenesTaxonomy(IEnumerable(Of Query), Dictionary(Of String, NamedValue(Of Int32)), Dictionary(Of String, otu_taxonomy), Double)

Create taxonomy assignment result and OTU aboundance data via gast algorithm.

Remarks

使用gast最多只能够注释到species，不能够具体的注释到某一个菌株？？

Parameters

Name	Type	Description
`blastn`	`IEnumerable(Of Query)`	the alignment result between the contigs and the greengenes reference sequence.
`OTUs`	`Dictionary(Of String, NamedValue(Of Int32))`	the OTU count table
`taxonomy`	`Dictionary(Of String, otu_taxonomy)`	taxonomy mapping from greengenes database.

method TreeAssign #

TreeAssign(Query, NamedValue(Of Int32), Dictionary(Of String, otu_taxonomy), Double)

Parameters

Name	Type	Description
`align`	`Query`	-
`OTU`	`NamedValue(Of Int32)`	-
`taxonomy`	`Dictionary(Of String, otu_taxonomy)`	-
`min_pct#`	`Double`	`[0-1]` or `[0-100]` 0.97 equals to 97