GBS barcode splitter statistics

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Protocols

GBS barcode splitter specifications

Information


Unique identifier OMICS_01050
Name GBS barcode splitter
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

GBS barcode splitter citations

 (5)
library_books

Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background

2017
PMCID: 5582342
PMID: 28912788
DOI: 10.3389/fpls.2017.01477

[…] university genomic facilities in august 2015 for library preparation (a psti enzyme was used) and sequencing. the raw data were demultiplexed and the illumina barcode removed using the software gbs barcode splitter (https://sourceforge.net/projects/gbsbarcode/). subsequently, the sequences were filtered at a 25 phred quality score and the illumina adapters removed with the fastq-mcf program […]

library_books

Eggplant Resistance to the Ralstonia solanacearum Species Complex Involves Both Broad Spectrum and Strain Specific Quantitative Trait Loci

2017
PMCID: 5437220
PMID: 28580001
DOI: 10.3389/fpls.2017.00828

[…] center., illumina adapter sequences were removed from raw reads and remaining reads were assigned to individual lines using barcode sequences (one specific barcode sequence for each line) with the gbs barcode splitter tool. barcode sequences were trimmed, unassigned reads were removed and remaining reads were trimmed to 90 bp. the stacks software v.1.28 () was used to identify single […]

call_split

An SNP based saturated genetic map and QTL analysis of fruit related traits in Zucchini using Genotyping by sequencing

2017
PMCID: 5241963
PMID: 28100189
DOI: 10.1186/s12864-016-3439-y
call_split See protocol

[…] including the parents and f1 (three replicates each) and 122 ril samples. gbs sequencing reads were de-multiplexed according to the sample barcodes and adapter sequences were removed using gbs barcode splitter []. reads were trimmed by base phred quality (q score < 25) and reads shorter than 30 base pairs were discarded before mapping and snp calling., the filtered, high-quality […]

library_books

Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing

2016
PMCID: 5213257
PMID: 28070306
DOI: 10.1002/ece3.2623

[…] assembled de novo and filtered again after assembly. paired‐end one (pe1) reads were processed separately for each of the two libraries (see discussion of pe2 reads, supporting information). gbs barcode splitter, other custom perl scripts, and fastx‐toolkit were used to sort samples by barcode, trim pe1 reads to 90 bps, and remove sequence reads that had more than 5% of their bases […]

library_books

Genotyping by sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus

2016
PMCID: 4864905
PMID: 27169718
DOI: 10.1186/s13104-016-2069-4

[…] platform flow cell (illumina, san diego, usa) using 101 single-end cycles., samples were initially de-multiplexed using custom perl scripts reported by elshire et al. [] and retrieved from the gbs barcode splitter site on sourceforge []. subsequently, data were analysed using stacks v1.29 [] running stacks denovo with default settings. the resultant genotype files were filtered […]


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