Virus Genome Sequencing Service
Viruses can be an important tool for delivering genes into cells either in vitro or in vivo studies. The process of packaging viral vectors into particles can often be imperfect, and package full-length or partial constructs. In some instances, host DNA can even be packaged into viral particles as well. As these vectors are beginning to be developed for therapeutic applications, the integrity of the packaged material is very important. abm is proud to now offer a Viral Genome Sequencing service that can process replication-incompetent Adenoviruses and AAVs to provide scientists with beneficial information for use in their research.
abm is an Illumina Certified Service Provider, dedicated to ensuring the delivery of the highest-quality data available for genetic analysis applications.
"I am a fan of abm: great product quality, great price, great rewards and great experience."Dr. Vincent Emond, Centre de recherche du CHU de Québec CHUL
|Paired-end sequencing||UNIT||CAT. NO.||Unit Price|
|Virus Genome Sequencing (up to 10 million reads, 2x75bp PE)||1 Sample||IL13007||$745.00|
|SERVICE NAME||UNIT||CAT. NO.||UNIT PRICE|
|Standard WGS Analysis||1 Sample||IB00011||$220.00|
|Reference Genome Import (<10Mb genome)||1 Genome||IB00001||$55.00|
|Reference Genome Import (>10Mb genome)||1 Genome||IB00002||$220.00|
|de novo Assembly
(<10Mb Genome, Minimum 100X coverage needed)
|de novo Assembly (>10Mb Genome)||1 Sample||IB00014||Inquire|
|SERVICE NAME||UNIT||CAT. NO.||UNIT PRICE|
|Sample and Library QC||Per Sample||IR18001||$55.00|
|Data Storage (per additional 3 months)||IS10001||$150.00|
|Hard Drive of NGS Results - Up to 2 Tb||1 Hard Drive||IS10003||$125.00|
Key Features for abm's Virus Genome Sequencing service
|Starting Material||2 x 1011 Viral particles|
|Sequencing Type||75 bp paired end sequencing.
Longer read lengths available upon custom request.
|Bioinformatics Analyses||Read alignment
SNP and Indel calling
de novo assembly (please consult us for sequencing depth)
Genome variation detection
|Turn-around Time||About 4-6 weeks from passing sample QC|
|Data Storage||3 months|
High quality assembly (shown by the dot plot on the leftt) enables accurate calling of SNPs, Simple Indels, and large Compound Variations. Circos plot (right) shows from outside to inside: Reference genome (brown), SNP density (green), Simple Deletion size (blue), Simple Insertion size (red), Compound Variation size (grey).
Project Design/Advice Assistance
Confidentiality and Service Policy
Our goal is always to deliver high-quality useful data to aid you in your research. We perform extensive maintenance and quality assurance on our equipment and strict quality control of samples throughout the sequencing process. However, next-generation sequencing by nature does not always deliver equally robust results due to a variety of factors, such as the variability inherent in the library preparation process, the biochemistry that takes place during sequencing and the quality of samples that we receive. We will make every effort to deliver the number of reads that are listed, although it is not possible to guarantee that those targets will always be achieved. The actual number of reads passing filter may vary by up to 10% from the listed target. Studies by various institutes have shown that there is minimal difference in coverage for 10% variation in reads past 5-10 million total reads.
All services are for research use only.
|Is your company certified as a service provider for Illumina Sequencing?|
Yes, we are a certified Illumina service provider.
|What kind of analysis software do you use for sequence analysis?|
The Illumina sequencers come with the integrated software that can perform the regular bioinformatics analysis functions. In addition, we have extensive experience with other open access software such as Galaxy, Adnuril, BioBike, etc. In other words, we are willing to perform additional bioinformatics analysis with different software and tools to satisfy a variety of demands from our customers.
|What kind of QC methods do you adopt for the customer's sample(s)?|
We will perform QC on your Total RNA samples prior to sequencing them, using the Agilent Bioanalyzer (industry standard) to determine the RNA Integrity Number (RIN). If the RIN is lower than 8, we consider these samples as having failed QC. If the samples do not pass QC, we will ask you to send us new samples. If we do not receive new samples, thereby cancelling the sequencing order, there will be a QC fee of $50/sample. This fee will be waived if you choose to continue with the sequencing order. A strict positive and negative control will be applied to this QC process. The library QC will also be performed using the Agilent Bioanalyzer to determine library size and purity. Also, prior to loading the libraries on the sequencer, we perform qPCR quantification. The cost for this is included in the sequencing service. For the QC of the final data from our sequencing service, the integrated software will generally do the job and provide adequate QC information, however, we can also provide additional QC data such as FASTQC upon request. The data we output will pass our Q30 filter, which means that the error rate in base calls is less than 1 in 1000, or 0.1%. We will get a percentage at the end of the run which states the percentage of bases that have a Q score > 30, and this percentage is usually ≥85%.
|What is the lead time for your WGS, WES, and RNA-Seq services?|
Our sequencing lead times depend on workload, but are typically 2-4 weeks for sequencing data + 2-3 weeks for standard analysis. Please inquire for lead times for more detailed analysis.
|01||Barclay, R. A. et al. "Exosomes from uninfected cells activate transcription of latent HIV-1." J. Biol. Chem 292(28):11682-11701 (2017). DOI: 10.1074/jbc.A117.793521. Application: RNA-Seq.|
|02||Ee, LS et al. "An Embryonic Stem Cell-Specific NuRD Complex Functions through Interaction with WDR5." Stem Cell Rep 8(6):1488-1496 (2017). DOI: 10.1016/j.stemcr.2017.04.020. Application: RNA-Seq.|
|03||Acharya, D et al. "KAT-Independent Gene Regulation by Tip60 Promotes ESC Self-Renewal but Not Pluripotency." Cell Rep 19(4):671-679 (2017). DOI: 10.1016/j.celrep.2017.04.001 .Application: RNA-Seq.|
|04||Goudarzi, R et al. "Effects of Arthrocen, an avocado/soy unsaponifiables agent, on inflammatory mediators and gene expression in human chondrocytes." FEBS Open Bio 7(2):187-194 (2017). DOI: 10.1002/2211-5463.12176. Application: RNA-Seq.|
|05||Taylor, J.F. et al. "In Vitro Effects of Arthrocen, an Avocado/Soy Unsaponifiables Agent, on Inflammation and Global Gene expression in Human Monocytes." IJC 9(4):31-39 (2017). DOI: 10.5539/ijc.v9n4p31. Application: RNA-Seq.|
|06||Alam, S.B. and Rochon, D. "Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection." J Virol 90 (7):3302-3317 (2016). DOI: 10.1128/JVI.02833-15. PubMed: 26719261. Application: RNA-Seq.|
|07||Ghoshala, K et al. "Encapsidation of Host RNAs by Cucumber Necrosis Virus Coat Protein during both Agroinfiltration and Infection." J Virol 89(21):10748-61 (2015). DOI: 10.1128/JVI.01466-15. PubMed: 26269190. Application: Next Generation Sequencing.|
|08||Nakamura, S et al. "Novel roles for LIX1L in promoting cancer cell proliferation through ROS1-mediated LIX1L phosphorylation." Sci Rep 5:13474: (2015). DOI: 10.1038/srep13474. PubMed: 26310847. Application: Next Generation Sequencing.|