Bioinformatics

Assembly and Annotation RNA Analysis Haploid Variant Calling Custom Analysis

SeqCenter was founded as an economic and expedient genomics sequencing service provider, but did you know that we also offer a variety of analytic services? Our skilled team of bioinformaticians address the most pressing needs of our customers, which are detailed on this page. These analytic services follow peer-reviewed industry standards and exclusively use open-source programs to ensure transparency and reproducibility.

Our goal is to provide meaningful data and preliminary analyses to help guide your experimental design. As with all bioinformatic analyses, these findings are considered predictive only and should be validated through empirical testing before proceeding to publication. To help you get started with the analysis of your sequencing data, we have curated a list of our most common basic analyses.

  • Assembly and Annotation Icon

    Assembly and Annotation

    As the volume of generated sequence data continues to expand, the scientific community has a responsibility to ensure that the data accurately reflects the genomic information of the host organism. At SeqCenter, we utilize rigorously reviewed tools to carry out de novo genome assemblies to capture this information. This analysis is valid for our Illumina, Oxford Nanopore, and PacBio sequencing packages for homogeneous samples, with some options for metagenomic samples.

    Explore
  • RNA Analysis Icon

    RNA Analysis

    RNA expression data has the power to show us the active functions within a cell moments before the suspension and isolation of RNA. Differential expression analyses can identify actively expressed genes and can elucidate the active metabolic functions within an organism at the time of sampling by accurately mapping, counting, and comparing sequenced RNA transcripts against a valid reference genome. This analysis is valid for our Illumina RNA sequencing packages.

    Explore
  • Haploid Variant Calling Icon

    Haploid Variant Calling

    Genomic changes at the cellular level can have a dramatic impact on the overall function and appearance of microbial communities and can provide evolutionary advantages. Mutations can be captured through whole genome sequencing and subsequent variant calling to identify SNPs, indels, and other mutations within monoclonal, haploid samples. For diploid or polyploid variant calling services, please contact us for custom analysis. This analysis is valid for our Illumina DNA sequencing packages and Oxford Nanopore WGS packages.

    Explore
  • Bioinformatics icon

    Custom Analysis

    The needs and demands of the scientific community rapidly adapt to innovations in technology and literature. At SeqCenter, our goal is to make genomic data accessible. If there is a custom bioinformatic project you would like to discuss with us, please click Explore to learn more. This analysis is valid for our Illumina, Oxford Nanopore, and PacBio sequencing packages.

    Explore

Contact:
91 43rd Street, Ste. 250
Pittsburgh, PA 15201
(878) 227-4915

Services:

About:

Resources:

Copyright 2024

Full Flowcell:

We offer full flowcell sequencing services for libraries that have been prepared outside of our lab. For each library, we will need to know the loading concentration, phiX spike-in, and run structure. Data is delivered as a complete run folder and can be demultiplexed upon request if a sample sheet is provided.

SARS-CoV-2 Sequencing:

Our SARS-CoV-2 Sequencing services include an assembly on the SARS-CoV-2 reference genome as a scaffold. These packages provide roughly 200Mbp of paired end reads (2×151 bp) as fastq files and the assembly in fasta format.

We require a minimum sample volume of 15 µL of extracted material (or 250µL for VTM samples) and recommend that only samples with Ct values below 35 are sent (because submissions are not measured for viral load before processing). We offer services for both purified RNA and samples in VTM media that require viral RNA extraction. Please see our SARS-CoV-2 Sequencing page for more detailed information.

Microbiome Sequencing:

Please see our Microbiome Sequencing page for package details, including distributables and sample requirements.

Nanopore Sequencing:

Our Oxford Nanopore sequencing packages provide reads equal to the length of input DNA, delivered as a fastq file.

For each sample, we require a minimum volume of 60 µL, and at least 40 ng/µL dsDNA quantified by Qubit or other dye-based method (100 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Long Read Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

PacBio:

Our PacBio services deliver HiFi reads with an average read length of 8-12kb for standard offerings and up to 25kb for full flowcell runs. All package names are listed by the minimum number of >Q20 reads that will be delivered. Both assembly and annotation are included with all packages.

For each sample, a minimum volume of 60 µL and at least 35 ng/µL dsDNA (quantified by Qubit or other dye-based methods) are required. SeqCenter strongly recommends utilizing our HMW DNA Extraction service for best results; however, we will also accept samples that are shipped on dry ice to avoid DNA integrity issues caused by the shipping process.

Please see our PacBio Sequencing page for more detailed information about our services.

RNA Sequencing:

We offer both rRNA depletion RNA squencing and polyA-tail enrichment mRNA sequencing. Both provide stranded, paired end reads (2x 151bp) as fastq files.

For each sample, we require a minimum volume of 20µL and at least 50ng/µL RNA. We also recommend, but do not require, that samples be DNAse treated and have a RIN score greater than 6. We also offer Basic and Intermediate RNAseq analyses, which require an annotated reference sequence.

Please see our RNA Sequencing page for more detailed information about both our RNA sequencing and analysis packages.

Illumina Sequencing:

The Illumina sequencing packages produce paired end reads (2×151 bp) delivered as fastq files.

For each sample, we require a minimum volume of 30 µL and at least 10 ng/µL dsDNA quantified by Qubit or other dye-based method (20 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Whole Genome Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

For additional information about variant calling and short read assemblies, please see our Bioinformatics page.

Go to Top