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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
The tools and their options comparing the percentage of demultiplexed reads and correctly trimmed reads from total reads, for paired-end and single end data. The GBSX option NA indicates an enzyme was not provided for demultiplexing. Sabre does not perform trimming and therefor has no trimming values in the plot.
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Fig3: The tools and their options comparing the percentage of demultiplexed reads and correctly trimmed reads from total reads, for paired-end and single end data. The GBSX option NA indicates an enzyme was not provided for demultiplexing. Sabre does not perform trimming and therefor has no trimming values in the plot.

Mentions: Overall, we find GBSX demultiplexing to be equal to Sabre and more sensitive than Stacks (Table 1 and Figure 3). GBSX and Sabre use a similar barcode recognition algorithm explaining their near identical results when not including the restriction enzyme recognition site. For GBSX, the demultiplexing of GBS and RAD data also use the same algorithm, as indicated by identical results. In addition, the barcode needed for the demultiplexing is always in the first read of paired-end data which means paired-end and single end read data should have identical results. This is true for GBSX and Sabre, but not Stacks. Stacks does filter reads on quality which could potentially cause discordance between single and paired-end analyses. Stacks had no misassigned barcodes, while GBSX misassigned less than one in a million reads when using a restriction enzyme recognition site and about four in a million without a restriction enzyme recognition site (due to a 4 bp shorter recognition site). Though GBSX introduces a very small number of misassigned barcodes, it does provide much greater sensitivity (GBSX >98% vs. Stacks 62/84%, Table 1) which we believe provides a more favorable demultiplexing tool.Figure 3


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

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

The tools and their options comparing the percentage of demultiplexed reads and correctly trimmed reads from total reads, for paired-end and single end data. The GBSX option NA indicates an enzyme was not provided for demultiplexing. Sabre does not perform trimming and therefor has no trimming values in the plot.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: The tools and their options comparing the percentage of demultiplexed reads and correctly trimmed reads from total reads, for paired-end and single end data. The GBSX option NA indicates an enzyme was not provided for demultiplexing. Sabre does not perform trimming and therefor has no trimming values in the plot.
Mentions: Overall, we find GBSX demultiplexing to be equal to Sabre and more sensitive than Stacks (Table 1 and Figure 3). GBSX and Sabre use a similar barcode recognition algorithm explaining their near identical results when not including the restriction enzyme recognition site. For GBSX, the demultiplexing of GBS and RAD data also use the same algorithm, as indicated by identical results. In addition, the barcode needed for the demultiplexing is always in the first read of paired-end data which means paired-end and single end read data should have identical results. This is true for GBSX and Sabre, but not Stacks. Stacks does filter reads on quality which could potentially cause discordance between single and paired-end analyses. Stacks had no misassigned barcodes, while GBSX misassigned less than one in a million reads when using a restriction enzyme recognition site and about four in a million without a restriction enzyme recognition site (due to a 4 bp shorter recognition site). Though GBSX introduces a very small number of misassigned barcodes, it does provide much greater sensitivity (GBSX >98% vs. Stacks 62/84%, Table 1) which we believe provides a more favorable demultiplexing tool.Figure 3

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