Whole Genome Sequencing
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Applied Biological Materials, Inc. is an Illumina Certified Service Provider, dedicated to ensuring the delivery of the highest-quality data available for genetic analysis applications. Click here for more details about the Illumina CSpro program.
  Whole genome data at your fingertips.

Prices are in US dollars. Please contact technical@abmgood.com if you need a quotation in Canadian dollars. Prices include sample QC, library preparation and quantification, and sequencing. Custom sequencing requirements can be quoted by contacting our technical support team.
Service/Description Cat. No. Min. Samples Price*
Whole Genome Sequencing (Paired-End)
Whole Genome Sequencing (1Gb, 2x75bp, PE) IW20100 2$485.00*
Whole Genome Sequencing (5Gb, 2x75bp, PE) IW20150 2$935.00*
Whole Genome Sequencing (10Gb, 2x75bp PE) IW20200 2$1485.00*
Whole Genome Sequencing (30Gb, 2x75bp PE) IW20400 2$3695.00*
Whole Genome Sequencing (60Gb, 2x150bp PE) IW20600 2$5385.00*
 
Bioinformatics Analysis
Raw data provided in FASTQ format if none of the below services are selected.
Note: abm is not responsible if there is an insufficient amount of reads to adequately perform an analysis.
Standard WGS Analysis
- read alignment
- De-duplication, base quality recalibration, and local realignment
- SNP and Indel calling
- Unified genome variation calling from genome assembly#
#Available with de novo genome assembly
IB00011 1$200.00*
de novo Genome Assembly
de novo Assembly (<10Mb Genome, Minimum 100X coverage needed) IB00013 1$300.00*
de novo Assembly (>10Mb Genome) IB00014 1Inquire
Genome annotation
- Gene prediction
- Repetitive element
- Functional annotation
IB00020 1$300.00*
Reference Genome Import
Free Reference Genome Import for Human or Mouse - Included
Reference Genome Import (<10Mb genome) IB00001 1$50.00^
Reference Genome Import (>10Mb genome) IB00002 1$200.00^
Other bioinformatics analyses available, please contact us for a quote.
 
Additional Sample Preparation Services
DNA Isolation for NGS IW19001 1$50.00*
 
Data Storage Service
Data Storage (per additional 3 months) IS10001 1$150.00
*Price per Sample
^Price per Species
Service Details
Description
    Whole Genome Sequencing (WGS) provides the most comprehensive map of an organism's genetic make-up. Unlike targeted or exome sequencing, WGS covers all corners of an organisms’ entire genome, which is arguably the most important molecular data. For bacteria, this approach is highly effective for studying virulence, drug resistance or novel drug targets. Similarly, comparative genomic for eukaryotes through resequencing or de novo assembly is the best approach to obtain high resolution genomic variations. High quality sequencing is now available with as little as 1 ng of starting material.

Key features for abm's WGS service
Sequencing Platform Illumina
Starting Material 50 ng (eukaryote) or 1 ng (prokaryote)
Sequencing Type 75 bp paired end.
Longer read lengths available upon customer request.
Library Type 500bp fragment size (average)
Larger fragment size available upon customer request.
Bioinformatics Analyses Read alignment
SNP and Indel calling
de novo assembly*
Unified genomic variation detection*
Turn-around Time 2-4 weeks for sequencing plus 2-3 weeks for analysis
Data Storage 3 months
*Offered with a minimum of 100X coverage.

abm’s WGS service overview:


Exploratory Bioinformatics Analyses:
    abm’s proprietary Unified Variation Caller detects genomic variation using an alignment-based and de novo assembly-based approach that is more sensitive and accurate in comparison to many popular choices such as VarScan, Pindel, and GATK. Our key advantage is the ability to accurately detect compound variations (deletions and insertions occurring at the same loci).


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).

Deliverables:
  1. Sequencing results in FASTQ format
  2. SNP and Indel calling
  3. Contig and scaffold sequences from de novo assemblies in FASTA format (if applicable)
  4. QC and analysis report

    All of abm's sequencing services are performed by a group of specially trained and experienced scientists partaking in a streamlined workflow.
    For more information, please contact our technical support team with details of your project requirements at technical@abmgood.com.
Sample Requirement Guidelines Click To Open
    Our technical support team will be happy to work on confirming the details of your NGS service. Please contact our specialists at technical@abmgood.com to get your order confirmation number. Any samples shipped to our facility without an order confirmation number in the attention line will be destroyed and disposed immediately upon receipt.
Coverage Guidelines Click To Open
Sample Submission Form Click To Open
Confidentiality
    All customer information is held in strict confidence. All materials and information sent to us and the products produced by us for the order are the property of the customer and will be returned to the customer or discarded in an confidential manner. We only archive customer materials when instructed to.
Project Design/Advice
    Please email NGS@abmgood.com for assistance with starting your sequencing project or for any inquiries relating to our Next Generation Sequencing services.
Product Documents
Product References
FAQs
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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.
Can you recommend any preferred RNA/DNA isolation kits to provide the best quality samples for these services?
For miRNA sequencing, you may isolate your RNA sample with a mirVana™ miRNA Isolation Kit,
mirVana™ PARIS™ Kit or PureLink® miRNA Isolation kit to enable adequate enrichment of your sample. If preferred, it should be okay to use Qiagen's kit, as long as the RNA Integrity Number (RIN) of the sample is above 8.0 to make sure there is no significant degradation. (Samples with a RIN lower than 8.0 may contain smaller degraded RNA fragments that can be sequenced in addition to the miRNAs). We prefer receiving Total RNA sample however so we can perform the bioanalyzer QC to check the RNA quality before beginning library construction. There will be no extra-charges if you submit Total RNA instead of isolated miRNA.

For miRNA sequencing we require 200ng-2ug of total RNA in 10ul of nuclease free water, as quantified with a fluorometric method. Lower amounts might result in inefficient ligation and low yield. If you are supplying purified miRNA, please submit a minimum of 50-100 ng of purified small RNA in 10ul is required. Purified small RNAs must be in nuclease free water or 10 mM Tris-HCI, pH 8.5.

For other services, there are generally no preferred DNA/RNA isolation kits as long as minimum requirements for QC are met.

Do I need any special software to view the data report files?
You will first need to unzip the fastq.gz files with winrar to view with vim, nano, gedit, Notepad plus plus. Nextgen workbench generally can view the data immediately without unzipping.

The RNASeq_sample_cufflinks_output.tar.gz will also need to be unzipped to see the text files by vim, nano, gedit, or Notepad plus plus. The unzipped data an also be imported as text into the data tab of Excel 2007. Other versions may differ.

To analyze further, Excel can sort, filter, find, match, etc and has many functions for conditional coloring, graphing, etc.
For the data, why are there no "ALT", "POS" and "ID" in your CSV file?
CSV files are meant to be used in conjunction with the raw fastq/bam files by certain commercial bioinformatics software. Many have a proprietary algorithms that takes the ALT POS and ID from the Fastq and indexes them for its own use. They are not meant to be used alone.
Would you let me know the description for the following: Genotype Sample_0, Coverage Sample_0, Coverage By Allele Sample_0, Variant Quality Sample_0, and Genotype Quality Sample_0?
Genotype (Sample Name) = nucleotide. Coverage (Sample Name) = will fail if there are insufficient reads. Coverage by allele (Sample Name) = will fail on one strand (+/-) read if only one side of the pair was sequenced. Variant Quality (Sample Name) = confidence of variant called. Genotype Quality (Sample Name) = confidence of genotype sequenced.
Concerning the column of "CHROM", would you let me know the rules of naming?
type of accession number| actual number| type of sequence| actual curated version used
Does your NGS service including RNA isolation?
We do not provide RNA isolation service by default. However we can provide this service. For more information, please refer to Cat#IR19001.
How many biological replicates do I need for each condition?
To increase confidence and reduce experimental error it is suggested that you submit at least 3 replicates per sample. Note that this is to serve as a guideline only and the final number of replicates and samples is to be determined by the end user based on their final experimental conditions.
Which kind of sequencer from Illumina do you have (HiSeq or MiSeq)?
We have both Illumina HiSeq and MiSeq platforms in use.
Can we identify SNPs or count number variants in specific genes for human samples?
If the Standard WGS Analysis is ordered, we can include the SNP and variant counts. You must let us know your preferred reference, our default is hg19/GRCh37.
What coverage does your WGS provide?
This will depend on what species the samples are. We can provide WGS for any species. For example, Bacteria and humans have vastly different genome sizes, giving different coverages.

For a quick solution, you can take the # gb in the service and divide by genome size to find out the amount of coverage that service will give:
eg. 30Gb = 30,000,000,000 bases.
If the genome size is 1Gb = 1,000,000,000 bases, 30Gb will give 30X coverage.

For human WGS, it's more around 3Gb for genome size, so 30Gb will give 10X coverage. For a list of coverages, please visit the "Coverage Guidelines" section on this page.
What species can we submit?
We can perform WGS on any species and there are no limitations.
What is the uniformity of coverages and what parts of genomes are uncovered under sequencing?
For WGS, we would fragment the genomic DNA, ligate adapters, and sequence them. It is difficult for us to predict the uniformity of coverage and what parts of the genomes are uncovered, as each sample and species is different.
Can you please clarify a bit more on the FASTQ and BAM data, and VCF?
FASTQ is raw data that comes out from the unit/computer after demultiplexing. Adapters are trimmed. Includes quality metrics of each read.

BAM refers to the compressed/mapped format of the above raw FASTQ data.

VCF is the processed file that expresses only the differences between the raw/compressed-mapped sample and a known reference; thus is much smaller. The differences are the SNP/mutation/indels that you would be looking for. This is the only file you can use to locate these genetic markers.

To visualize the vcf file, you need to upload it to a visualizer like UCSC (https://genome.ucsc.edu/) or have your own visualizing program like genome in a box, galaxy, etc.

The level of annotation is often higher in UCSC [sic] but uses a 0-based coordinate system and is sometimes listed as hg19/GRCH37; But that is an older version of what NCBI uses right now. The current version is hg19/GRCh38 and uses a 1-based co-ordinate system.

Often this is important if the user already has an established data pool/collaborators/etc and wishes to compare annotations between old and new data. In most labs starting out, it will not matter which you use so long as they import/identify the correct reference into your visualization tool and be consistent with it so you can report comparable data.
For Bacterial WGS, how should I ship my samples if I require ABM to perform the DNA extraction?
The bacterial cells should be spun down in a 1.5mL tube, the media should be removed, and the cell pellet should be shipped frozen on dry ice. Ideally, we will need a minimum of 1 million cells, however the more cells you are able to provide, the better.
Does your whole genome sequencing service sequence the whole genome, i.e. all the nuclear DNA, introns and exons, and all the mitochondrial DNA?
Yes