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

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Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts).
 
Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts).
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[[Category:Ada:NGS]]

Revision as of 15:32, 15 June 2016

Data Normalization, Clustering & Collapsing

BBNorm

GCATemplates available: no

BBNorm homepage

 module load 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 load 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 load 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).