Tablet pipeline

Tablet specifications

Information


Unique identifier OMICS_00896
Name Tablet
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License BSD 2-clause “Simplified” License
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline David Marshall <>

Publications for Tablet

Tablet IN pipelines

 (25)
2017
PMCID: 5214804
PMID: 28070453
DOI: 10.7717/peerj.2733

[…] as previously described (heylen et al., 2015). obtained reads were mapped against g1p[8] reference strain wa using mira 3.4 (chevreux et al., 2004) and assemblies were visually inspected in tablet (milne et al., 2013). subsequently the consensus sequences for 9 gene segments of rotarix™ were determined, used for further analysis and deposited in genbank under accession numbers: […]

2017
PMCID: 5378975
PMID: 28345654
DOI: 10.1038/ncomms14822

[…] reads were mapped with novoalign version 2.07.14 to the williams 82 genomic sequence, resulting in a bam file for each soybean line with the samtools48. the sequences were analysed with a tablet viewer49 and an igv viewer50 for the building of consensus sequences, and the manual calling of snps and indels using the williams 82 genomic sequence as a reference sequence., a total of 81 […]

2017
PMCID: 5483232
PMID: 28552360
DOI: 10.1016/j.cub.2017.05.023

[…] mitogenome (nc_012920); for this step, we used samtools mpileup and the option -s to specify the ploidy (1). only bases with quality scores ≥ 30 were considered for analysis. furthermore, we used tablet [95] to visualize the alignments and checked by eye all the polymorphic positions reported in the vcf file. variants called at positions with less than 3 reads of depth, as well as variants […]

2017
PMCID: 5502847
PMID: 28684566
DOI: 10.1128/genomeA.00515-17

[…] reads according to standard illumina protocols. the total reads (6,540,291) were mapped to a reference sequence (accession no. jq944705) using bwa (version 0.7.5a-r405) (5) and was visualized in tablet (6). a modified samtools/vcfutils (7) script was used to generate an intermediate consensus sequence in which any indels relative to the original reference sequence were appropriately called. […]

2017
PMCID: 5504624
PMID: 28693578
DOI: 10.1186/s12917-017-1135-z

[…] related full length eblv-2 genome available (germany 2012 – genbank accession number ky688149). reads were mapped using the burrow-wheeler aligner (bwa version 0.7.5a–r405) [38] and visualized in tablet [39]. a modified samtools/vcfutils [40] script was used to generate an intermediate consensus sequence in which any indels and snps relative to the original reference sequence […]

Tablet institution(s)
Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK
Tablet funding source(s)
Scottish Government (RERAD, Programme 1); the Scottish Funding Council and Scottish Enterprise through the Scottish Bioinformatics Research Network (SBRN) project

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