SILVA_OTU

Full name SMRUCC.genomics.Analysis.Metagenome.SILVA_OTU Assembly SMRUCC.genomics.Analysis.Metagenome Members 3

01 Syntax

SMRUCC.genomics.Analysis.Metagenome.SILVA_OTU

02 Methods

Name	Overloads	Summary
ParseOTUrep	1
RemovesOTUlt	1	Removes all of the OTU that counts less than cutoff percentage.
OTUsilvaTaxonomy	1	Assign OTU taxonomy from OTU blastn against silva database with votes

03 Members

method ParseOTUrep #

ParseOTUrep(IEnumerable(Of FastaSeq))

Parameters

Name	Type	Description
`fasta`	`IEnumerable(Of FastaSeq)`	通过mothur的GetOTUrep 命令获取得到的OTU代表序列的fasta文件数据

method RemovesOTUlt #

RemovesOTUlt(Dictionary(Of String, NamedValue(Of Int32)), Double)

Removes all of the OTU that counts less than cutoff percentage.

Parameters

Name	Type	Description
`OTUrep`	`Dictionary(Of String, NamedValue(Of Int32))`	Loaded fasta header data from mothur `get.oturep` output.
`cutoff#`	`Double`	The sequence number cutoff percentage.

method OTUsilvaTaxonomy #

OTUsilvaTaxonomy(IEnumerable(Of Query), Dictionary(Of String, NamedValue(Of Int32)), Double)

Assign OTU taxonomy from OTU blastn against silva database with votes

Parameters

Name	Type	Description
`blastn`	`IEnumerable(Of Query)`	-