Tablet protocols

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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

 (28)
2018
PMCID: 5827183
PMID: 29520294
DOI: 10.3389/fgene.2018.00046

[…] to find open reading frame (orf) regions. these approaches allowed us to locate microsatellites in coding sequences (cds) or untranslated regions (5′utr and 3′utr) through graphical sequence viewer tablet (milne et al., )., dna was extracted from fin fragments using the wizard genomic dna purification kit (promega), according to the manufacturer's protocol. microsatellite validation […]

2018
PMCID: 5946053
PMID: 29748409
DOI: 10.1128/genomeA.00403-18

[…] contig, which was joined to other contigs manually by pcr and sanger sequencing. the reads were assembled against the resulting contig by using bowtie 2 () and viewed by using tablet (). the genome ends were identified from two large sets of reads sharing an end. the reconstructed genome was 149,343 bp in size and consisted of a unique region of 100,111 bp flanked […]

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

[…] and sequenced using 454™ gs-flx pyrosequencing as previously described (). obtained reads were mapped against g1p[8] reference strain wa using mira 3.4 () and assemblies were visually inspected in tablet (). subsequently the consensus sequences for 9 gene segments of rotarix™ were determined, used for further analysis and deposited in genbank under accession numbers: kx954616– kx954624., […]

2017
PMCID: 5418769
PMID: 28472937
DOI: 10.1186/s12864-017-3709-3

[…] curated for inconsistencies. to estimate the sequencing depth of each base, bowtie v. 1.0.0 was used to align illumina reads onto the assembled mitogenomes. aligned reads were viewed using igv, tablet, pysamstats (v. 0.84) and bamstats (v. 1.25) [–]. heteroplasmic sites were identified using three conditions: first, different nucleotides were sequenced in the same position; second, […]

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 [] 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 […]


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Tablet in publications

 (97)
PMCID: 5946053
PMID: 29748409
DOI: 10.1128/genomeA.00403-18

[…] contig, which was joined to other contigs manually by pcr and sanger sequencing. the reads were assembled against the resulting contig by using bowtie 2 () and viewed by using tablet (). the genome ends were identified from two large sets of reads sharing an end. the reconstructed genome was 149,343 bp in size and consisted of a unique region of 100,111 bp flanked […]

PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] bwa version 0.7.5a-r405 [], and pacbio reads with bwa-sw v0.7.14-r1138 long query read, mismatch penalty 5, gap open penalty 2, gap extension penalty 1, z-best 10. alignments were viewed in igv [], tablet version 1.16.09.06 [] and samtools tview version 0.1.19-96b5f2294a []., genome nucleotide pairwise distance was calculated with genometools version 1.5.8 genomediff []. andi [], with kimura […]

PMCID: 5924567
PMID: 29690652
DOI: 10.3390/genes9040225

[…] errors were corrected manually using consed []. the purity of the scaffolds was also checked against the genome of t. aegyptius dsm 12793. possible miss-assemblies were corrected manually using tablet, a graphical viewer for the visualisation of assemblies and read mappings []. based on these analyses, the high-quality permanent genome that was obtained was only half the size (3,093,245 bp) […]

PMCID: 5883640
PMID: 29615108
DOI: 10.1186/s40168-018-0452-1

[…] kit wizard® dna clean-up system. sequencing was performed with the ion proton sequencing technology. alignment of obtained reads was performed using bowtie2 (-n 1 –l 32) and then visualized with tablet, using default parameters []. we obtained 204,837 reads mapping to the a2-165 genome, of which 19,702 and 30,274 reads aligned to the lagaffe and mushu prophages respectively., quantification […]

PMCID: 5832266
PMID: 29494671
DOI: 10.1371/journal.pone.0193682

[…] []. unrelated contigs were removed. viral contigs not matching the reference were kept. ambiguous nucleotides in the de novo assembly contigs were manually curated by visualizing read alignments in tablet []., the pedv strain v215-78 was from the fli virus collection, it was obtained from within europe in 1978 and was grown in vero cells. there is no information available about the virulence […]


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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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