GBS barcode splitter protocols

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GBS barcode splitter statistics

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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

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GBS barcode splitter in pipelines

 (3)
2017
PMCID: 5241963
PMID: 28100189
DOI: 10.1186/s12864-016-3439-y

[…] 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 […]

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 […]

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 […]


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GBS barcode splitter in publications

 (4)
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 […]

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 […]

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 […]

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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