GBSX protocols

View GBSX computational protocol

GBSX specifications

Information


Unique identifier OMICS_08632
Name GBSX
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
BioPerl
Maintained Yes

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Documentation


Maintainer


  • person_outline Jeroen KJ Van Houdt <>

Publication for GBSX

GBSX in pipeline

2017
PMCID: 5688169
PMID: 29142201
DOI: 10.1038/s41598-017-15816-5

[…] on an illumina hiseq. 2500, rapid-run mode, single-end 100 base reads, at duke center for genomics and computational biology., after unzipping fastq.gz files to fastq files by gunzip command, the gbsx package was used for demultiplexing of reads. reads were organized into new files with adapter sequences removed, reads were discarded that were, shorter than 50 bases, and trim leading […]


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GBSX in publications

 (3)
PMCID: 5830781
PMID: 29515892
DOI: 10.1098/rsos.171901

[…] separately, employing parameters previously identified as maximizing matching snp calls and minimizing mismatching snp calls between sample replicates. raw sequencing reads were demultiplexed using gbsx []. these demultiplexed reads were chastity filtered, had regions with quality less than q10 trimmed from either end of the read, had cut-sites removed, had adapters removed (allowing for one […]

PMCID: 5688169
PMID: 29142201
DOI: 10.1038/s41598-017-15816-5

[…] on an illumina hiseq. 2500, rapid-run mode, single-end 100 base reads, at duke center for genomics and computational biology., after unzipping fastq.gz files to fastq files by gunzip command, the gbsx package was used for demultiplexing of reads. reads were organized into new files with adapter sequences removed, reads were discarded that were, shorter than 50 bases, and trim leading […]

PMCID: 5670326
PMID: 29163587
DOI: 10.3389/fpls.2017.01860

[…] adegenet 2.0.0., identification of significant dmms between regions was then computed using the package msgbsr (accessed on 26/08/2016). in brief, raw sequencing data was first demultiplexed using gbsx () and filtered to remove any reads that did not match the barcode sequence used for library construction. following demultiplexing, paired-end reads were merged using bbmerge in bbtools package […]


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GBSX institution(s)
Center for Human Genetics, KU Leuven, Herestraat, Leuven, Belgium

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