Article

Tablet - Next Generation Sequence Assembly Visualization

Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK.
Bioinformatics (Impact Factor: 4.98). 12/2009; 26(3):401-2. DOI: 10.1093/bioinformatics/btp666
Source: PubMed

ABSTRACT

Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine.
Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions.
Contact: tablet@scri.ac.uk

Download full-text

Full-text

Available from: Paul Shaw
    • "Assembly of SPVC reads produced a contig of 10 793 nt, which also covered over 99% of its complete genome (accession number KF386015), with a mean sequence coverage of 267-fold, which was higher in the 3 0 terminus than in the 5 0 terminus. Examination of SPFMV-O and SPFMV-RC and SPVC assemblies using TABLET software (Milne et al. 2010) showed no evidence of the presence of multiple common single nucleotide polymorphisms (SNPs), suggesting that all the viral isolates were identical at such position, which suggests that the viral isolates do not display quasi-species behaviour. The comparison of the new SPFMV-O, SPFMV-RC and SPVC sequences assembled in this study with the existing genomes (ACC:AB465608, D86371 and AB509453, respectively ) suggests that SPFMV-O sequence lacks 17 bases at the 5 0 end, whereas the SPFMV-RC sequence lacks 8 bases and SPVC sequence lacks 37 bases. "

    No preview · Article · Jan 2016
  • Source
    • "The mitogenomes were annotated using the web-based services MitoFish and MITOS [1] [3] and features in protein-coding genes were analyzed according to Temperley et al. [9]. In order to estimate the support of each base in the mitogenomes, Bowtie v. 1.0.0 was used to align the reads of each fish on its own assembled mitogenome, and this mapping was viewed using the Integrated Genome Viewer (IGV) or the Tablet [10] [4] [5] [8]. Heteroplasmic sites were detected using IGV, setting the software to show positions in which the frequency of the second most frequent base was equal to or higher than 10% and the total reads number were higher than 100. "
    [Show abstract] [Hide abstract]
    ABSTRACT: This data-set complements our paper entitled "The use of transcriptomic next-generation sequencing data to assembly mitochondrial genomes of Ancistrus spp. (Loricariidae)" [6]. Here, we present the nucleotide sequences of each transcript used for mitogenomes assembly, as well as tables presenting the location of each transcript in the mitogenomes; the frequency, location and codon position of the detected heteroplasmic sites; and the start/stop codons usage, UTR, CDS and poliA-tail length for each protein coding gene. Readers are referred to the paper cited above for data interpretation and discussion.
    Full-text · Article · Dec 2015
  • Source
    • "The nature of the detected polymorphisms and their frequency are stored as output results (Figure 2F). Visual checking of the detected and not considered false positives were done using the Tablet software (Milne et al. 2009) for " .ACE " alignment files and with the Jalview software (Waterhouse et al. 2009) for " .FASTA " files. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from Next Generation Sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying Single Nucleotide Polymorphisms (SNPs), and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger-(re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, which were initially predicted by our program). The rDNA domains of S. maritima have similar lengths to those found in other Poaceae, apart from the 5'-ETS which is about twice longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), while high intra-genomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by Fluorescent In Situ Hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be employed at any ploidy level and using different sequencing technologies.
    Preview · Article · Nov 2015 · G3-Genes Genomes Genetics
Show more