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Plugin

Duplicate Reads Removal

The duplicate reads removal plug-in is designed to filter out duplicate reads. This tool is specifically well-suited to handle duplicate reads coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.

Latest improvements

  • The detection method is now faster and scales better. However, the sensitivity to sequencing indel errors has increased.

Changes

  • The detection method is now faster and scales better. However, the sensitivity to sequencing indel errors has increased.

Duplicate Reads Removal Tool

The purpose of the tool is to reduce the data set to include only one copy of the duplicate sequence. The challenge is to achieve this without removing identical or almost identical reads that would arise from high coverage of certain regions, e.g. repeat regions or highly expressed exons from transcriptome sequencing. The algorithm takes sequencing errors into account when removing the duplicates.

The approach taken here is based on the raw sequencing data without any knowledge about how they map to a reference sequence. This means that this is well-suited for both de novo assembly and resequencing purposes.

The plug-in is available both for the CLC Genomics Workbench and the CLC Genomics Server.

Known Limitations

In its current version, the duplicate read removal has a limitation when there are duplicate reads that contain several alleles. The algorithm will identify that there are duplicate reads to be removed, but it is not able to distinguish between sequencing errors and true variation in the reads. So if you have a heterozygous SNP in such an area, you may risk that only one of the alleles are preserved. We are working on improving the algorithm to handle this.

Screenshots

The Looks

Guides

Further Reading

Installation

The plugin is easily installed from within the Workbench:

  1. Click Plugins in the Toolbar
  2. Click the tab Download Plugins
  3. Select the plugin you wish to install
  4. Click the Download and Install button

Download from www.clcbio.com

Alternatively, you can download the plugin.

Workbench Download Server Download