Custom Analysis
While we are not a dedicated Bioinformatic service provider, we do strive to serve our customers by finding the analysis services that are right for their research goals. If you have a project in mind that is more involved than our standard offerings, please reach out to us with a description of the work that you would like performed. Currently, we do have some custom bioinformatic support available, but we are also gladly able to put you in contact with outside bioinformatic consultation service providers who may able to help you with analysis requests outside the scope of SeqCenter’s services. Please review some of our most common custom offerings below.
Illumina Sequencing (Analysis Add-Ons) |
Price* |
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Basic RNA Analysis Using a GenBank file or an NCBI accession number as a reference (required), we generate counts data for coding sequences across the Eukaryotic and Prokaryotic genomes for downstream analyses. See the RNA Analysis page for more information. |
$20.00 |
Intermediate RNA Analysis This service includes the Basic RNA Analysis and extends it by evaluating the counts data across samples in your order to identify differentially expressed genes. This pairwise comparison can also identify metabolic pathway changes if the provided reference is in the KEGG curated pathway database. See the RNA Analysis page for more information. |
$40.00 |
Haploid CNV Analysis In an evaluation of read coverage across a genome, sequenced reads can be aligned against a reference (required) in either GenBank/Fasta format or as an NCBI accession. Similar to the RNA analyses, the generated counts data can provide information on copy number variation (CNV) within a sample. This pipeline is currently applicable for Prokaryotic samples and select fungal species. |
$40.00 |
Haploid Variant Calling Analysis (BreSeq) Reads are aligned against a reference (required) to identify SNPs and InDels. References provided as Fasta files will receive an interactive list of base-pair changes while annotated references such as GenBank files will receive a list of mutations and the encoded consequence on the amino acid sequence. This pipeline is currently applicable for Prokaryotic samples and select fungal species. See the Haplotype Variant Calling page for more information. |
$10.00 |
Diploid Variant Calling Analysis (GATK Haplotype Caller) Eukaryotic organisms benefit from this diploid variant calling analysis package where reads are compared to a provided reference (required) and a generated variant call file (VCF) file is provided. Organisms present in the SnpEff Ensemble database such as the GRCh38.p14 genome are eligible for a functional annotation of the identified variants, producing an annotated VCF file.Example uses: Diverse metagenomes, small algae |
$50.00 |
Enriched Viral Assembly This service requires additional lab services to be eligible to continue. Viral/phage samples that undergo enrichment at SeqCenter can be aligned to a customer provided reference and the sequence can then be inferred. This service requires an eligible reference and an eligible BED file to trim enrichment primer sites. Outside data may be considered on a case-by-case basis but is subject to the Outside Data Formatting Fee. |
$10.00 |
Short Read Assembly and Annotation If you would like to add on an assembly to previously generated Illumina data, we can carry out a de novo assembly using unicycler and a subsequent annotation using Bakta (Prokaryotes) or Funannotate (Fungi). This service is not typically recommended for Eukaryotic organisms and is best for samples that are being compared to a publication-quality reference. This will generate an early-draft contig assembly. To reconcile the assembly with a known reference, please contact us about our Reference Guided Scaffolding service. See the Assembly and Annotation page for more information. |
$20.00 |
Hybrid Assembly and Annotation (with Nanopore Data) If you would like to add on an assembly to previously generated Illumina and Nanopore data, we can carry out a de novo assembly of the long reads using Flye and subsequently polish the reads with the Illumina data. See the Hybrid Assemblies page for more information. See the Assembly and Annotation page for more information. |
$30.00 |
Shotgun Metagenomic Analysis (≤1Gbp) This service runs a metagenomic assembly and subsequently bins assembled contigs into taxonomically distinct groups. Taxonomic identity is then evaluated using Kraken2 for the original reads in the analysis, as well as the bins resulting from the assembly. Each analysis includes the taxonomic report, a Krona phylogeny of taxa within a sample, and annotations of the binned data. See the Shotgun Metagenomics page for more information. |
$40.00 |
Shotgun Metagenomic Analysis (1 Gbp – <5 Gbp) See the Shotgun Metagenomics page for more information. |
$50.00 |
Shotgun Metagenomic Analysis (5 Gbp – <10 Gbp) See the Shotgun Metagenomics page for more information. |
$80.00 |
Shotgun Metagenomic Analysis (10 Gbp – <25 Gbp) See the Shotgun Metagenomics page for more information. |
$125.00 |
Oxford Nanopore Sequencing (Analysis Add-Ons) |
Price |
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Hybrid Assembly and Annotation (with Illumina Data) If you would like to add on an assembly to previously generated Illumina and Nanopore data, we can carry out a de novo assembly of the long reads using Flye and subsequently polish the reads with the Illumina data. See the Hybrid Assemblies page for more information. See the Assembly and Annotation page for more information. |
$30.00 |
Haploid Variant Calling Analysis (Pepper) Reads are compared to a provided reference (required) and a generated alignment file (BAM) and variant call file (VCF) file are provided. |
$20.00 |
Diploid Variant Calling Analysis (DeepVariant) Reads are compared to a provided reference (required) and a generated alignment file (BAM) and variant call file (VCF) file are provided. |
$70.00 |
Haploid CNV Analysis In an evaluation of read coverage across a genome, sequenced reads can be aligned against a reference (required) in either GenBank/Fasta format or as an NCBI accession. Similar to the RNA analyses, the generated counts data can provide information on copy number variation (CNV) within a sample. This pipeline is currently applicable for Prokaryotic samples and select fungal species. |
$40.00 |
PacBio Sequencing (Analysis Add-Ons) |
Price |
---|---|
Haploid Variant Calling Analysis (Pepper) Reads are compared to a provided reference (required) and a generated alignment file (BAM) and variant call file (VCF) file are provided. |
$20.00 |
Diploid Variant Calling Analysis (DeepVariant) Reads are compared to a provided reference (required) and a generated alignment file (BAM) and variant call file (VCF) file are provided. |
$70.00 |
AAV Analysis Add on AAV analyses are available for data externally generated from SeqCenter. Our current AAV Sequencing services using the PacBio instruments already include this service. See the PacBio AAV page for more information. |
$50.00 |
Prokaryotic Assembly and Annotation If you would like to add on an assembly to previously generated PacBio data, we can carry out a de novo assembly using Flye. See the Assembly and Annotation page for more information. |
$30.00 |
Eukaryotic Assembly and Annotation See the Assembly and Annotation page for more information. |
$50.00 |
Methylation Calling Add-on (4mC and 6mA) This services requires an assembly and annotation. To capture 4mC and 6mA motifs in your assembly, you can add on the methylation calling services. This analysis aligns the raw kinetics data against your assembly to identify putative methylation sites. Please note that this can only be selected as an assembly add on and requires the presence of kinetic information in the generated PacBio data which is not enabled on instrument by default. |
$20.00 |
Additional Fees and Services (Analysis Add-Ons) |
Price |
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Reference Guided Scaffolding If you have attempted the de novo assembly and the resulting contigs are not providing the coverage that you are looking for, reference guided scaffolding may help. Here we can either correct an existing de novo assembly or generate a new de novo assembly and then correct it using a reference (required). This will allow us to align the start sites, trim chromosomes that are misassembled, and backfill gaps using the provided reference. By default, we will only backfill with “N” characters to preserve the integrity of the de novo assembly. In general, this correction is only recommended if you are confident that the species are closely related. We may adjust the price if an assembly already exists. This service includes the de novo assembly, the scaffolding, and subsequent annotation. |
$60.00 |
PGAP Annotation Setup Fee To use the PGAP Annotation tool for Prokaryotic samples in place of the Bakta annotation tool (our default), we charge a one-time setup fee per PGAP configuration file for each order. Subsequent annotation would then use PGAP instead of Bakta. Additional purchase of an assembly and annotation is required. |
$10.00 |
AMRFinderPlus Analysis This is an add on service for Prokaryotic annotations to provide an additional file of antimicrobial resistance genes. This is priced out per sample. Additional purchase of an assembly and annotation is required. |
$10.00 |
Average Nucleotide Identity (ANI) Analysis This is an add on service for existing assemblies. Final assembled content is compared against a reference (required) provided as either a .fasta or a .gbk file. |
$10.00 |
IS Compare Analysis This is an add on service for existing assemblies to identify or validate targeted insertions or rearrangements. This pipeline is exclusive to prokaryotic samples only. A reference for the organism without the insertion is required (.fasta or a .gbk file) in addition to the insertion sequence (.fasta). |
$10.00 |
Kraken2 Analysis – Community Sample This analysis provides data similar to the initial steps of our shotgun metagenomics pipeline. Required inputs are Fastq files to identify the taxa within a given sample. Generated files include the Kraken report, the Kraken analysis file, and a generated Krona phylogeny graph of the identified samples. |
$20.00 |
StrainScan – Monoculture Similar to the community profile, this analysis is applicable for single strain samples where a species ID is desired. The output is the StrainScan report. Since this tool will use a custom database to carry out the strain identification, an NCBI species level taxonomy ID is required. |
$20.00 |
Kraken2 Analysis – Monoculture Similar to the community profile, this analysis is applicable for single strain samples where a species ID is desired. The output is the Kraken report. |
$10.00 |
MetaPhlAn Analysis – Monoculture Similar to the community profile, this analysis is applicable for single strain samples where a species ID is desired. The output is the MetaPhlAn report. |
$10.00 |
Centrifuge Analysis – Monoculture Similar to the community profile, this analysis is applicable for single strain samples where a species ID is desired. The output is the Centrifuge report. |
$10.00 |
Outside Data Formatting Fee If any of these bioinformatic services are being requested for data generated outside of SeqCenter, we will add a mandatory formatting fee. This allows us to determine if the provided data is eligible for the selected analysis and adjust any nomenclature or characters that are not compatible with SeqCenter bioinformatic pipelines. |
$10.00 |
Hourly Custom Bioinformatic Services Are you looking for an analysis or service that is not listed here? We accept custom projects on a case-by-case basis and require a peer-reviewed publication that details the analysis you would like us to carry out. Custom services are billed in 15-minute increments starting at $200 per hour. |
$200.00 |
Contact:
91 43rd Street, Ste. 250
Pittsburgh, PA 15201
(878) 227-4915
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