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GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments.

Herten K, Hestand MS, Vermeesch JR, Van Houdt JK - BMC Bioinformatics (2015)

Bottom Line: To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized.Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.

View Article: PubMed Central - PubMed

Affiliation: Center for Human Genetics, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. koen.herten@med.kuleuven.be.

ABSTRACT

Background: Massive parallel sequencing is a powerful tool for variant discovery and genotyping. To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized. This technology is generally referred to as Genotyping By Sequencing (GBS). To deal with GBS experimental design and initial processing specific bioinformatic tools are needed.

Results: GBSX is a package that assists in selecting the appropriate enzyme and the design of compatible in-line barcodes. Post sequencing, it performs optimized demultiplexing using these barcodes to create fastq files per barcode which can easily be plugged into existing variant analysis pipelines. Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.

Conclusions: GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.

Show MeSH
Library types with in-line barcode. The GBSX demultiplexer can handle barcode only sequences, sequences starting with barcode and restriction enzyme site (RS), and those that also end with RS and/or common adapter.
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Fig1: Library types with in-line barcode. The GBSX demultiplexer can handle barcode only sequences, sequences starting with barcode and restriction enzyme site (RS), and those that also end with RS and/or common adapter.

Mentions: However, the restriction based reduction introduces low-diversity in the initial bases of the sequencing library due to every sequence starting with an identical restriction digest recognition sequence. This interferes with (Illumina) cluster identification, resulting in a significant loss of data [7-10]. A solution to this problem is the addition of in-line barcodes (Figure 1) with different lengths. The length difference ensures that the restriction digest recognition sequence, present in all library fragments, is not read in the same sequencing cycle.Figure 1


GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments.

Herten K, Hestand MS, Vermeesch JR, Van Houdt JK - BMC Bioinformatics (2015)

Library types with in-line barcode. The GBSX demultiplexer can handle barcode only sequences, sequences starting with barcode and restriction enzyme site (RS), and those that also end with RS and/or common adapter.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4359581&req=5

Fig1: Library types with in-line barcode. The GBSX demultiplexer can handle barcode only sequences, sequences starting with barcode and restriction enzyme site (RS), and those that also end with RS and/or common adapter.
Mentions: However, the restriction based reduction introduces low-diversity in the initial bases of the sequencing library due to every sequence starting with an identical restriction digest recognition sequence. This interferes with (Illumina) cluster identification, resulting in a significant loss of data [7-10]. A solution to this problem is the addition of in-line barcodes (Figure 1) with different lengths. The length difference ensures that the restriction digest recognition sequence, present in all library fragments, is not read in the same sequencing cycle.Figure 1

Bottom Line: To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized.Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.

View Article: PubMed Central - PubMed

Affiliation: Center for Human Genetics, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. koen.herten@med.kuleuven.be.

ABSTRACT

Background: Massive parallel sequencing is a powerful tool for variant discovery and genotyping. To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized. This technology is generally referred to as Genotyping By Sequencing (GBS). To deal with GBS experimental design and initial processing specific bioinformatic tools are needed.

Results: GBSX is a package that assists in selecting the appropriate enzyme and the design of compatible in-line barcodes. Post sequencing, it performs optimized demultiplexing using these barcodes to create fastq files per barcode which can easily be plugged into existing variant analysis pipelines. Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.

Conclusions: GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.

Show MeSH