Category Archives: Sequencing

Single Molecule Sequencing and Genome Assembly of a Clinical Specimen of Loa loa

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Scientists Apply Successful Single Molecule Sequencing and de novo Genome Assembly to a Parasitic Worm that Infects Human Eyes and Skin

Investigators at the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine and the Laboratory of Parasitic Diseases at the National Institute of Allergy and Infectious Diseases (NIAID) at the National Institutes of Health (NIH) used the long-read, single-molecule Pacific Biosciences platform for the successful genome sequencing and de novo assembly of Loa loa round worms from a clinical sample. Their research, which generated the most complete genome sequence of a filarial nematode produced to date, provides a more comprehensive reference genome for this parasite in the hopes of developing better molecular diagnostics to decrease morbidity from filarial nematodes. Their findings appear in today’s issue of BMC Genomics.

Click here to access the abstract and complete article.

GRC Awarded Contract to Expand FDA Microbial Genome Database

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IGS and the GRC have been awarded a contract to assist the U.S. Food and Drug Administration (FDA) in the expansion and curation of a public database of microbial genome sequences and associated metadata. This will serve as a valuable reference to evaluate and assess high-throughput sequencing based diagnostic devices. In addition to all publicly available microbial genome sequences, the database will include more than 550 newly sequenced, assembled, and annotated genomes from under-represented branches of the phylogenetic tree. For more information on the project, please click here or contact the GRC.

GRC Posters Presented at AGBT 2014

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This year we are highlighting some of the work we’ve done in the past year.

The first poster provides an overview of how changes to our PacBio pipeline have increased our sequencing yields and read lengths, resulting in finished, high-quality microbial genomes, assembled using only PacBio data.

The second poster demonstrates how Next Gen sequencing can be used to investigate host and pathogen associations in cases of pulmonary non-tuberculous mycobacterial (PNTM) infections.

For more information on our full range of sequencing and analysis services, visit our Laboratory Services and Analysis Services pages. Please contact us if you have any questions.

PacBio Pipeline Off to a Strong Start for 2014

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It has been a busy January for our PacBio RSII instrument. We are excited to report a new record yield from a single SMRT cell – 896,457,524 passed filter bases! It seems we are not far off from hitting 1 G.

 

Some more stats from this cell:

                Mean Read Length: 8391 bp

                P50 Subread Length: 6187 bp

                P90 Subread Length: 12314 bp

                P95 Subread Length: 14032 bp

                Maximum Subread Length: 24585 bp

 

We have come a long way in the past year. Here is a comparison of yields and mean read lengths of our top 20 SMRT cells in January 2013, compared to our top 20 SMRT cells so far in 2014:

The increases in both SMRT cell yields and read lengths are making PacBio an attractive option for sequencing and finishing microbial genomes. We are excited to see where 2014 will take us!

For more information on our full range of sequencing and analysis services, visit our Laboratory Services and Analysis Services pages. Please contact us if you have any questions.

Finishing Genomes with the PacBio RS II – Read our Core Lab Profile

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The GRC, which offers services from sequencing library prep through genome assembly and downstream analysis, is generating complete bacterial genome sequences and methylation profiles using PacBio SMRT sequencing on the RS II. Several advancements in the library prep, sequencer, sequencing protocols, and data analysis software have all contributed to this.

To learn more about these breakthroughs and other emerging applications of SMRT sequencing, please read the PacBio Core Lab Profile showcasing the research performed at GRC and IGS here.

GRC and IGS offer not only cutting-edge sequencing, but a complete menu of services including assembly, annotation, and custom analyses. For more information about services offered, visit our Laboratory Services and Analysis Services pages. Please contact us if you have any questions.

 

Increasing PacBio RS II SubRead Lengths

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Although the latest SMRTcell has been designed to shift the loading bias towards larger read lengths, when working with long insert libraries (10-20 kb), the preferential loading of smaller fragments often limits the potential of these libraries.

A solution to this is to remove small fragments from the libraries. We have evaluated the Blue Pippin (Sage Science, Inc., Beverly MA), an automated electrophoresis system that separates and collects DNA fragments based upon their size, for this purpose.

In order to measure the increase in subread length, long insert libraries were prepared with fragments larger than 4 kb or 7 kb isolated using the Blue Pippin and a 0.75% Agarose Gel Cassette (BLF7510) and compared to a library without Blue Pippin size selection. As shown below, the removal of smaller library fragments prior to sequencing increases the average length of the library fragments loaded into ZMWs on the SMRTcell.

In addition to longer subreads, there is also a boost to the amount of data generated per ZMW. As the fragment length increases, the percentage of SMRTbell adapter sequence decreases and the percentage of library insert increases. The graph below shows the average number of passed-filter bases per active ZMW versus the average fragment length of each library. Using Blue Pippin size selection, we have achieved yields of >500 M passed filter bases from individual SMRTcells.

Below are the sequencing and assembly results of four genomes sequenced from long-insert, Blue Pippin size-selected libraries. Using only PacBio long subread data, we were able to assemble complete microbial genomes for three of the four isolates. Even with only a single under-loaded and low-yield SMRTcell, the remaining isolate still resulted in a nearly complete genome assembly with 10 total contigs and >60% of the genome assembled in the largest contig.


PacBio RSII producing encouraging early results

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Our PacBio throughput and read lengths have been improving steadily over the past year and may have just taken yet another big step forward.  We upgraded our PacBio sequencer to RSII in mid-May and we are seeing significant increases in per-cell yield and improved read lengths with our longer libraries.  The most notable change in the upgrade from RSI to RSII is the doubling of the number of simultaneously observable sequencing reactions on the SMRTcell, allowing throughput to be effectively doubled as well.  Let’s take a look at some examples:

In this comparison of an 8kb Mycobacterium library that was run both before and after the upgrade, we see an almost 3x increase in total yield per-SMRTcell, while read lengths remain about the same.

Below is a comparison of per-SMRTcell stats from multiple libraries across multiple organisms, including both 8kb and 14kb libraries from Mycobacterium sp., Plasmodium falciparum, Saccharomyces cerevisiae and Candida albicans.  Driven by the longer libraries, we see both dramatically higher yield and longer read lengths. On one recent 8 SMRTcell run of a 14kb library, we saw an average per-SMRTcell yield of 417 Mbp!

Here is a read length plot comparing the runs from the table above:

 Although we are early in our use and optimization of the new PacBio RSII, we are encouraged by the increase in both yield and read length, and expect continued improvement in our PacBio data, subsequently improving data analysis and genome assembly.

Highly Multiplexed 16S Sequencing on MiSeq

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16S amplicon sequencing has proven to be an important tool for identifying and quantifying microbes present in metagenomic samples. We have several researchers here at IGS who have used this to analyze organismal and environmental communities for several years.

Together with these researchers, the GRC has been working over the past year to transition high-throughput sequencing of 16S rRNA regions amplified from metagenomic samples from the 454 platform to the Illumina platform. With the increased read length (2x250bp) on the MiSeq, it is now well suited to generate 16S data for a fraction of the cost of generating data on the 454 FLX.

A typical 16S amplicon run on the 454 produces ~1M reads with an average read length of ~500 bp, which enables deep profiling of 100-200 samples. A paired-end MiSeq run generates 500 bp of sequence per amplicon and produces an average of 12M read pairs per run. We are now routinely profiling a minimum of 400 samples per run with even greater depth than possible on 454 for less than half the per-sample cost.

Please contact us for more information about our 16S profiling service using the Illumina MiSeq.

Complete microbial genomes using only PacBio data? Testing HGAP…

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We’ve spent some time recently testing a new way to assemble PacBio data called HGAP, which stands for “hierarchical genome assembly process”.  Unlike previous assemblers of PacBio data that have relied on the use of either Illumina and/or PacBio CCS reads for error correction of PacBio long reads, HGAP uses multiple alignments of all reads to perform the corrections, potentially eliminating the need for other libraries and data types.  The corrected reads are assembled with an overlap-layout consensus assembler (in this case Celera Assembler) to form contigs.  More details about HGAP can be read found here: https://github.com/PacificBiosciences/DevNet/wiki/Hierarchical-Genome-Assembly-Process-%28HGAP%29

We have evaluated HGAP on several of our projects and compared it to our assembly of illumina-corrected Pacbio reads assembled with Celera Assembler.  So far, the results have been very encouraging and we have seen significant improvement in many cases.  The chart below shows several examples:

So the assemblies are more contiguous, but are the corrections good enough to generate accurate consensus sequence? In an attempt to verify the consensus accuracy of these HGAP assemblies for several Bordetella genomes, we aligned >240x coverage of 250bp Illumina MiSeq data to the HGAP-generated contigs and looked for discrepancies and SNPs using GATK. We found no cases of high-quality, passed-filter variants, which supports a highly accurate consensus sequence generated by the HGAP assembly.  We continue to test and compare HGAP with other PacBio assembly methods but are encouraged by initial results.