New kids on the show – who will be the winner?

Next Generation Sequencing is still a quite young market. Therefore we face the same situation every year: there is a lot of innovation going on in regard to new technologies, new instruments and other inventions. Amongst all these innovations GenomeWeb picked out the new platforms and asked in a survey about the expectancies in the market.

Instruments that were part of this survey are (at least in one of several questions):

  • Oxford Nanopore’s MinIon
  • Illumina’s X-Ten
  • Illuminas NextSeq 500
  • QIAGEN’s GeneReader
  • Life Technologies’ Ion Torrent PGM
  • Illumina HiSeq

Here are some of the results:

  • 35% of the participants say that the MinIon has the greatest impact on the sequencing community
  • 30% of the participtants will purchase most likely the NextSeq 500
  • Illumina HiSeq / MiSeq outperform the Ion Torrent Proton / PGM in data accuracy and throughput, the Ion Torrent instruments are better in respect of run time and instrument price

Read the complete survey here.

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NGS Applications – get an insight…

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You want to know more about projects where your research colleagues used next generation sequencing?

Check out the Nature Reviews overview of interesting publications releated to different applications of next generation sequencing.

Whose genome has been sequenced? Aquila chrysaetos

de-novo-sequencingEvery day an unimaginable number of NGS data is generated. Anyhow the number of avian genomes that have been sequenced so far is still quite small (Doyle et al table 1). Doyle et. al added one more avian genome to this list – the “Golden Eagle” Aquila chrysaetos.

What was sequenced?

A male golden eagle (Aquila chrysaetos canadensis) captured in the southern Sierra Nevada.

Sequencing strategy: Whole genome sequencing

  1. Libraries & Sequencing: 1 channel 2x 100 bp SG paired-end sequencing and 1 channel 2x 100 bp mate-paired sequencing using the Illumina HiSeq platform
  2. Data output: 68.4 Gb of raw data (25.3 Gb from the SG and 43.1 Gb from the mate-pair library). Total genome size (incl mtDNA) ~ 1.28 Gbp. Overall genome coverage ~ 40x. Longest scaffold: 11,517,212 bp
  3. Results: The mtDNA genome is characterised by 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The annotation produced a total of 16,571 predicted nuclear genes.

Besides the nuclear genome Doyle et al could also assemble the complete mitochondrial genome. Furthermore they found ~ 800,000 novel polymorphisms. These polymorphisms can now help to define markers that are involved in carnivory orother biological processes.

Read the complete publication here.

Whose Genome Has Been Sequenced? – Recent posts:

All you need to know about NGS

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During my research through the web for news in the area of NGS I found this great practical course:

The EMBL-EBI offers a 15h online course that should help every newby and everyone who needs some refreshing information in NGS. And since we have several users of this blog that are new to NGS I thought it would be worth to share this course.

This course is divided into several subunits so everyone can learn in his own speed and in alignment with other tasks that are on everyone’s desk.

 

The key learnings are:

  • Understand some principles behind NGS
  • Know the challenges created by NGS
  • Know how to submit and retrieve NGS data to and from databases
  • Understand the uses of NGS data in: Whole genome assembly; Gene expression analysis; Genome annotation; Gene regulation analysis; Variation studies

Thank you EMBL-EBI for this great summary!

Analysis of oaks using RAD-Seq

Excellent paper just out that dissects the phylogeny of North American oak trees using RAD-Seq.sequences-per-individual

A phylogenetic study of the American Oak clade based on RAD-seq data has recently be published by PLoS ONE. The study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23-33 million year-old clade.
Associated with the paper is a new R package for downstream analysis of phylogenetic RADseq data, RADami

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data >>

Are you a NGS expert?

Some months ago we asked you for how long you have been involved with next generation sequencing.

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Almost 200 people sent their feedback and gave us a very interesting insight in their experience with NGS. To take this into account, we want to further align our posts with the focus topics of our readers.

Feel free to send me your comments and suggestions to make ngs-expert.com even more valuable for you.

The next step after sequencing: Synthesis of a designer chromosome

Next generation sequencing allows deciphering genomes of any kind and size; But, what to do with all this information?

Now a group of scientists from the John Hopkins University in Baltimore around Jef Boeke and 79 other authors published that they have been able to synthesize one of the 16 chromosomes of the baker’s yeast. Instead of the natural 317,000 bases they have reduced the chromosome to 274,000 bases by leaving out what they regarded as redundant or not necessary to grow under cell culture conditions.

Yeast cells already today produce important substances in large fermenters. They are used for bio fuel production but also for the production of Artemisinin, a potent malaria drug.

By reducing the genome of such organisms, the perfect “factory” can be designed in the future that delivers high yield of the desired substance at a minimum cost and a minimum contamination with other undesired metabolic byproducts. The White Biotechnology is certainly a hope for our permanent growing population. A number of companies engaged in this field can be found here.

Why should I buy Illumina stock shares?

What is the impact for a company of winning an award? In case of Illumina you can cleary see it is about brand and market awareness. Only recently we reported about the award for Illumina of beeing the smartest company in 2013. Today we have a short interview for you that answers the question: why to buy stock shares for Illumina.

From my point of view the only risk of being a market leader in a highly dynamic area like next generation sequencing is, that you have a lot to loose. But Illumina is working on this. One example: only this year Illumina launched two new next generation sequencing instruments: the X-Ten for human whole genome sequencing and the Next500 – a mid-size sequencer that fills the gap between the HiSeq and the MiSeq. So let’s see what happens next…

Will Oxford Nanopore´s MinION hold its promises?

When I first heard of the Oxford Nanopore technology, it sounded rather exciting: The company proclaimed a new technology which enabled sequencing with extremely long read lengths of up to 100 kbp at a reasonable accuracy and in a very short time.

The technology is based on so-called “strand sequencing”. This technique involves a protein nanopore, in combination with a specific enzyme. This enzyme is designed to feed a single strand of DNA through the nanopore. The bases of the DNA strand are identified as they pass through the pore.

The sequencing systems are called “GridION” and “MinION”, with the GridION representing a high throughput system, and the MinION being a miniaturised system the size of a USB stick.

NewsFirst data for the GridION system have been presented in February 2012 at the AGBT conference. After that, there had been hardly any news from Oxford Nanopore for a long time. Then in November 2013, Oxford Nanopore announced an early access program for the MinION system on the ASHG meeting. They also gave demonstrations of the system to selected customers in the company´s labs. However, the company did not show any sequencing data yet. In February 2014, Oxford Nanopore has started to issue invitations to the early access program, and the first MinION systems should be shipped soon.

On the AGBT meeting in Feburary, the first MinION sequencing data, generated by Oxford Nanopore and analysed by David Jaffe from Broad Institute, Cambridge, have finally been presented.  However, the first results were rather disappointing: The average read length was way below the expectations. As reported by In Sequence, Jaffe told that the average read lengths were 5.4 kbp and 4.9 kbp for the two bacterial genomes analysed. The raw error rate of the data was not disclosed. However, Jaffe said that there were “long perfect stretches” and “blocks of errors”.  The data was not suitable for de novo assemblies from MinION data alone. In the end, the researchers used the sequences to create better assemblies from Illumina data.

On a Plant Genomics Meeting in Kuala Lumpur in the end of February, Oxford Nanopore Technologies presented more data. They claim that they could “easily obtain” 50 kbp reads. They had generated reads spanning the entire 48 kbp bacteriophage lambda genome. They also show data to underline that the read length distribution obtained by Nanopore sequencing is determined by the size distribution of the input DNA. Slides of the presentation can be viewed here.

Even if the first results are somewhat disappointing, I think this is still an interesting new technique. Like it was with the PacBio system, the technology may need more time to overcome its childhood diseases. The next few months will show if the technology can hold the high expectations that have been raised.