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Difference between revisions of "Bioinformatics:Data Normalization.2C Clustering .26 Collapsing"

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= NGS: Data Normalization, Clustering & Collapsing =
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= Data Normalization, Clustering & Collapsing =
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[https://hprc.tamu.edu/wiki/Bioinformatics Back to Bioinformatics Main Menu]
 
__TOC__
 
__TOC__
== BBNorm ==
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{{:SW:BBNorm}}
[[Ada:GCATemplates|GCATemplates]] available: no
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{{:SW:CD-HIT}}
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{{:SW:FASTX-Toolkit}}
  
BBNorm [https://sourceforge.net/projects/bbmap/ homepage]
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[[Category:Bioinformatics]]
 
 
  module spider BBMap
 
 
 
bbnorm.sh is the data normalization script that is part of the BBMap package.
 
 
 
BBNorm: Kmer-based error-correction and normalization tool.
 
 
 
 
 
== CD-HIT ==
 
[[Ada:GCATemplates|GCATemplates]] available: no
 
 
 
CD-HIT [http://weizhongli-lab.org/cd-hit/ homepage]
 
 
 
  module spider CD-HIT
 
 
 
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
 
 
 
 
 
== FASTX-Toolkit ==
 
[[Ada:GCATemplates|GCATemplates]] available: no
 
 
 
FASTX-Toolkit [http://hannonlab.cshl.edu/fastx_toolkit/ homepage]
 
 
 
  module spider FASTX-Toolkit
 
 
 
The fastx_collapser tool is included in the FASTX-Toolkit.
 
 
 
Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts).
 
 
 
[[Category:Ada:NGS]]
 

Latest revision as of 13:32, 3 December 2021

Data Normalization, Clustering & Collapsing

Back to Bioinformatics Main Menu

BBNorm

GCATemplates available: no

BBNorm homepage

 module spider BBMap

bbnorm.sh is the data normalization script that is part of the BBMap package.

BBNorm: Kmer-based error-correction and normalization tool.

CD-HIT

GCATemplates available: no

CD-HIT homepage

 module spider CD-HIT

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

FASTX-Toolkit

GCATemplates available: no

FASTX-Toolkit homepage

 module spider FASTX-Toolkit

The fastx_collapser tool is included in the FASTX-Toolkit.

Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts).