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Nextgen Bioinformatic Services

Palmerston North, Manawatu, NZ

At NgBS we specilise in providing flexible bioinformatic solutions at the best possible price. Let us take care of the technical challanges associated with Nextgen sequencing so that you can focus on what really matters - answering your research question!

Please note we do not provide a sequencing service.

Publications

  • The biosynthesis of nitrous oxide in the green alga Chlamydomonas reinhardtii. M Plouviez, D Wheeler, A Shilton, M Packer, P McLenachan, et al. The Plant Journal 91 (1), 45–56
  • The venom gland transcriptome of the parasitoid wasp Nasonia vitripennis highlights the importance of novel genes in venom function A Sim, D Wheeler. BMC Genomics 17 (571)
  • Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. JB Benoit, ZN Adelman, K Reinhardt, A Dolan, M Poelchau, EC Jennings, et al. Nature communications 7, 10165
  • A novel intracellular... Show more »

At NgBS we specilise in providing flexible bioinformatic solutions at the best possible price. Let us take care of the technical challanges associated with Nextgen sequencing so that you can focus on what really matters - answering your research question!

Please note we do not provide a sequencing service.

Publications

  • The biosynthesis of nitrous oxide in the green alga Chlamydomonas reinhardtii. M Plouviez, D Wheeler, A Shilton, M Packer, P McLenachan, et al. The Plant Journal 91 (1), 45–56
  • The venom gland transcriptome of the parasitoid wasp Nasonia vitripennis highlights the importance of novel genes in venom function A Sim, D Wheeler. BMC Genomics 17 (571)
  • Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. JB Benoit, ZN Adelman, K Reinhardt, A Dolan, M Poelchau, EC Jennings, et al. Nature communications 7, 10165
  • A novel intracellular mutualistic bacterium in the invasive ant Cardiocondyla obscurior. A Klein, L Schrader, R Gil, A Manzano-Marín, L Flórez, D Wheeler, et al. The ISME journal 10 (2), 376-388
  • A new approach for investigating venom function applied to venom calreticulin in a parasitoid wasp. AL Siebert, D Wheeler, JH Werren Toxicon 107, 304-316
  • A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor. C Zhao, LN Escalante, H Chen, TR Benatti, J Qu, S Chellapilla, et al. Current Biology 25 (5), 613-620
  • Nasonia vitripennis venom causes targeted gene expression changes in its fly host. EO Martinson, D Wheeler, J Wright, AL Siebert, JH Werren. Molecular ecology 23 (23), 5918-5930
  • Heterochromatin protein 1 expression is reduced in human thyroid malignancy. MS Tretiakova, SD Bond, D Wheeler, A Contreras, M Kocherginsky, et al. Laboratory Investigation 94 (7), 788
  • Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. JH Xiao, Z Yue, LY Jia, XH Yang, LH Niu, Z Wang, P Zhang, BF Sun, et al. Genome biology 14 (12), R141
  • Function and evolution of DNA methylation in Nasonia vitripennis
    X Wang, D Wheeler, A Avery, A Rago, JH Choi, JK Colbourne, AG Clark, et al. PLoS genetics 9 (10), e1003872
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Bioinformatics
Price on request
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Biology
Amplicons
ChIP-Seq
RNA-Seq
Genomics
Variant Calling
Whole Exome Sequencing
whole genome bisulfite sequencing
16S rDNA sequencing
Assembly
RNA Sequencing
Price on request

RNA-seq is a robust method for quantifying gene expression levels based on short read data. As a standard service we offer two of the most popular workflows DESeq2 and Cufflinks. If you are unsure of which application best suites your research question be sure to check out the FAQ below or contact us for additional advice. We will... Show more »

RNA-seq is a robust method for quantifying gene expression levels based on short read data. As a standard service we offer two of the most popular workflows DESeq2 and Cufflinks. If you are unsure of which application best suites your research question be sure to check out the FAQ below or contact us for additional advice. We will happily help you choose the tool that best addresses your research question.

As a minimum we would recommend three replicates per treatment group. For an 'average' Eukaryotic genome the ENCODE standard recommendation is for a minimum of 20 million reads per replicate, however robust quantification of low expressed genes or alternative splice forms could require up to 70 million reads per replicate. For Prokaryote transcriptomes we recommend 5 million reads per replicate. Pair-end data is normally not required for prokaryote RNA-seq due to the absence of splicing. Please see the FAQ for additional experimental considerations.

Outputs your will receive with a typical project

  • Differential expression calls with statistical support
  • Functional annotations (if available)
  • Heatmaps of differentially expressed genes
  • Clustering and Principle component analysis of replicates and treatments
  • Aligned reads in the form of BAM files suitable for viewing using visulisation tools (for example IGV).
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Human
Microbes
Yeast
Mouse
Cufflinks
Cuffdiff
Zebrafish
C. elegans
Drosophila
Biology
RNA-Seq
Genomics
mRNA-seq
miRNA-seq
DEseq
EdgeR
Amplicon Sequencing
Price on request

Amplicon projects use nextgen sequencing technologies to deeply sequence PCR products. Typically these PCR products are generated using universal primers that target ITS regions or 16S/18S ribosomal RNA genes, with the goal of using these markers to characterise the number and type of species found in each sample.

In contrast... Show more »

Amplicon projects use nextgen sequencing technologies to deeply sequence PCR products. Typically these PCR products are generated using universal primers that target ITS regions or 16S/18S ribosomal RNA genes, with the goal of using these markers to characterise the number and type of species found in each sample.

In contrast Metagenomic projects randomly sequence genomic fragments found in biological samples. These random fragments are then assembled and annotated to reveal molecular and metabolic pathways that can help define the functional properties of the community/sample.

At NgBS we offer as a standard amplicon service the QIIME pipeline. For metagenomics we offer a service based on the MEGAN/DIAMOND workflow.

Typical outputs that can be delivered

  • Taxonomic overview of samples
  • Comparisons between samples
  • Alpha and beta diversity estimates
  • QIIME web tools for data exploration
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Qiime
Amplicons
Human Gut Microbiome
Environmental samples
Microbial Isolates
16S rDNA sequencing
vsearch
Transcriptome assembly
Price on request

Accurate and complete genome assembly using nextgen sequencing data remains a significant challenge. This is especially so for large complex Eukaryotic genomes. The best assemblies are generated from sequencing performed on a mix of paired-end and mate-paired libraries. Ideally the mate-paired libraries also contain a range of... Show more »

Accurate and complete genome assembly using nextgen sequencing data remains a significant challenge. This is especially so for large complex Eukaryotic genomes. The best assemblies are generated from sequencing performed on a mix of paired-end and mate-paired libraries. Ideally the mate-paired libraries also contain a range of insert sizes ( ie 2, 5, 10kb). Once a genome has been assembled it is often favourable to generate gene model predictions to help identify features of interest. These gene models not only describe important gene features such as open reading frames, promoter positions, and exon-intron boundaries, they are also often essential for many downstream applications such as mutation detection and gene expression analysis.

For transcriptome assemblies high quality pure RNA is a key step in obtaining a robust snapshot of gene expression under the conditions being investigated. As part of our transcriptome assembly workflow we are also able to annotate the resulting transcripts and/or carry out differential expression analysis if you have data from different cell types or treatments.

BTW if you have PacBio data (great), we can help there as well!

Typical outputs that can be delivered

  • Fasta file containing your assembly
  • Annotation and gene model prediction
  • Comparison to closely related species
  • Differential expression analysis
  • Assembly statistics (N50, L50 etc)
« Show less
Microbes
Yeast
Drosophila
Insect
Biology
Genomics
oasis
trinity
Metagenomics
Price on request

Amplicon projects use nextgen sequencing technologies to deeply sequence PCR products. Typically these PCR products are generated using universal primers that target ITS regions or 16S/18S ribosomal RNA genes, with the goal of using these markers to characterise the number and type of species found in each sample.

In contrast... Show more »

Amplicon projects use nextgen sequencing technologies to deeply sequence PCR products. Typically these PCR products are generated using universal primers that target ITS regions or 16S/18S ribosomal RNA genes, with the goal of using these markers to characterise the number and type of species found in each sample.

In contrast Metagenomic projects randomly sequence genomic fragments found in biological samples. These random fragments are then assembled and annotated to reveal molecular and metabolic pathways that can help define the functional properties of the community/sample.

At NgBS we offer as a standard amplicon service the QIIME pipeline. For metagenomics we offer a service based on the MEGAN/DIAMOND workflow.

Typical outputs that can be delivered

  • Taxonomic overview of samples
  • Comparisons between samples
  • Alpha and beta diversity estimates
  • QIIME web tools for data exploration
« Show less
NGS data analysis
Next generation sequencing data analysis
Price on request
Request a quote for more information about this service.
DNA Assembly
Price on request
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Microbes
Yeast
Drosophila
Insect
Biology
Genomics
abyss
velvet
Whole Genome Bisulfite Sequencing
Price on request
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SNP Calling
Price on request

At NgBS we are able to identify variation in DNA sequences by mapping short read data to a reference genome. The variant callers we typical use are freebayes and/or samtools. Both of these programs are able to call single nucleotide polymorphisms as well as identify indels.

We are also able to functionally annotate variants... Show more »

At NgBS we are able to identify variation in DNA sequences by mapping short read data to a reference genome. The variant callers we typical use are freebayes and/or samtools. Both of these programs are able to call single nucleotide polymorphisms as well as identify indels.

We are also able to functionally annotate variants (i.e. identify SNPs that change amino acids or indels that cause frame-shift errors etc) if a set of gene models are available. We can also call SNPs using both callers and provide a file that only contains 'robust' SNPs that are called by both programs. We strongly recommend that you visually confirm any SNPs of interest using a viewer like IGV (we can help with this).

Typical outputs that can be delivered

  • Variant call information in the form of a VCF file
  • SNP statistics
  • If requested SNP annotations (coding mutations)
  • Short read alignment BAM files ready for viewing using visualisation tools (ie IGV)
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Biology
Genomics
freebayes
samtools
varscan
Genotyping Services
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DNA Sequencing
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Epigenetic Analysis
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Biology
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Biostatistics & Bioinformatics
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Sequencing Data Analysis
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Nucleic Acid Analysis
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Nucleic Acid Data Analysis
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Next Generation Sequencing
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DNA Synthesis
Price on request
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DNA
Price on request
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RNA
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Computational & Statistical Analysis
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Biochemistry & Molecular Biology
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Nucleic Acid Services
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