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


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 in 32- and 64-bit versions.

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    • "The sequencing depth of each base was verified using Bowtie v. 1.0.0 to align the reads to the mitogenome. This mapping was visualized using the Integrated Genome Viewer (IGV) (Langmead et al., 2009; Milne et al., 2009; Robinson et al., 2011; Thorvaldsdóttir et al., 2013). Heteroplasmic sites were detected using IGV by setting the software to show positions in which more than one nucleotide was sequenced, and that the frequency of the second most frequent base was equal to or higher than 5%. "
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    ABSTRACT: Hypoptopoma incognitum is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of H. incognitum with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.
    Mitochondrial DNA 09/2015; DOI:10.3109/19401736.2015.1079903 · 1.21 Impact Factor
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    • "The resulting linear scaffolds were further inspected using bwa and SAMtools (Li et al. 2009; Li and Durbin 2009) mapping all reads to the assembly and inspecting the .bam file using the tablet v. genome viewer (Milne et al. 2010) to look for regions of uneven coverage, Ns, or unpaired reads suggestive of assembly errors. Because the 16S rRNA gene was found in two separate contigs at 99% similarity, BLAST searches were performed for several other genes and this showed the same pattern, suggesting the presence of two strains of Xiphinematobacter. "
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    ABSTRACT: Bacterial mutualists can modulate the biochemical capacity of animals. Highly co-evolved nutritional mutualists do this by synthesizing nutrients missing from the host's diet. Genomics tools have advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (phylum Verrucomicrobia) from the dagger nematode Xiphinema americanum, a migratory ectoparasite of numerous crops that also vectors nepovirus. Previously, this endosymbiont was identified in the gut, ovaries and eggs, but its role was unknown. We explored the potential role of this symbiont using fluorescence in situ hybridization (FISH), genome sequencing, and comparative functional genomics. We report the first genome of an intracellular Verrucomicrobium and the first exclusively intracellular non-Wolbachia nematode symbiont. Results revealed Xiphinematobacter had a small 0.916 Mbp genome with only 817 predicted proteins, resembling genomes of other mutualist endosymbionts. Compared with free-living relatives, conserved proteins were shorter on average, and there was large-scale loss of regulatory pathways. Despite massive gene loss, more genes were retained for biosynthesis of amino acids predicted to be essential to the host. Gene ontology (GO) enrichment tests showed enrichment for biosynthesis of arginine, histidine, and aromatic amino acids, as well as thiamine and coenzyme A, diverging from the profiles of relatives Akkermansia muciniphilia (in the human colon), Methylacidiphilum infernorum and the mutualist Wolbachia from filarial nematodes. Together, these features and the location in the gut suggest Xiphinematobacter functions as a nutritional mutualist, supplementing essential nutrients that are depleted in the nematode diet. This pattern points to evolutionary convergence with endosymbionts found in sap-feeding insects.
    Genome Biology and Evolution 09/2015; DOI:10.1093/gbe/evv176 · 4.23 Impact Factor
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    • "The mitogenomes were annotated using the web-based services MitoFish and MITOS (Bernt et al., 2013b; Iwasaki et al., 2013). In order to estimate the support of each base of 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 (Langmead et al., 2009; Milne et al., 2009; Robinson et al., 2011; Thorvaldsdóttir et al., 2013). 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. "
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    ABSTRACT: Mitochondrial genes and genomes have long been applied in phylogenetics. Current protocols to sequence mitochondrial genomes rely almost exclusively on long range PCR or on the direct sequencing. While long range PCR includes unnecessary biases, the purification of mtDNA for direct sequencing is not straightforward. We used total RNA extracted from liver and Illumina HiSeq technology to sequence mitochondrial transcripts from three fish (Ancistrus spp.) and assemble their mitogenomes. Based on the mtDNA sequence of a close related species, we estimate to have sequenced 92%, 95% and 99% of the mitogenomes. Taken the sequences together, we sequenced all the 13 protein-coding genes, two ribosomal RNAs, 22 tRNAs and the D-loop known in vertebrate mitogenomes. The use of transcriptomic data allowed the observation of the punctuation pattern of mtRNA maturation, to analyze the transcriptional profile, and to detect heteroplasmic sites. The assembly of mtDNA from transcriptomic data is complementary to other approaches and overcomes some limitations of traditional strategies for sequencing mitogenomes. Moreover, this approach is faster than traditional methods and allow a clear identification of genes, in particular for tRNAs and rRNAs.
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