Questions and Answers 29 June.pdf

Question: How many DNA extractions are required?

Answer: We require 50 individual DNA extractions.

Question: How many library preps are needed?

Answer: We require one library per pool (5 libraries total).

Question: How much data is required for each pool?

Answer: We require roughly 15 Gb raw sequence data per pool.

Question: The solicitation specifies sequencing 5 pools of 10 samples each at 20x coverage, including alignment, variant calling, and filtering for an HD set of 30k–60k. Could you confirm if this also involves generating the panel itself? While we can manage this, providing an accurate quote for the panel requires more details about the anticipated volume and frequency of recurring work. We utilize hybrid capture panels with NGS for this purpose—does this meet your requirements?

Answer: Yes, the development and validation of an HD marker panel are the core deliverables. We require a fixed-content genotyping panel with a marker set designed to nest existing low-density loci, so stakeholders can choose among panel tiers at a consistent cost/density. Can you use the hybrid-capture NGS approach to generate a reproducible 30–60k SNP genotyping panel? If so, describe how a hybrid capture panel can be converted to a fixed array that is compatible with our needs. This is a one-time development eƯort (single-panel design); we do not anticipate recurring genotyping work, as the samples for panel development and validation will be sent in a single batch.

Question: To proceed, we will need a reference sequence. I located a potential resource, but it is only at the contig level. While we can use it, we strongly recommend generating a phased chromosome-level assembly using updated PacBio Revio data combined with Hi- C/Omni-C data for scaƯolding. We can include pricing for this if it is of interest. If you have another reference sequence available, please share its details so we can confirm its compatibility.

Answer: The resource you mentioned (NCBI GenBank Accession GCA_040938265.2) is our current reference genome assembly. Please note that the first 26 contigs are scaƯolds, while the last 5 are unplaced contigs. No, we do not require Hi-C data at this time.

Question: The solicitation mentions incorporating existing markers into the panel. Can you confirm whether this information will be provided to us?

Answer: Yes, we will provide the existing low-density data.

Question: The RFQ includes the addition of sex-linked markers. We have significant experience with QTL mapping across various organisms, including sex determination, and a dedicated research team specializing sex determination genetics. To map this trait, we will need specific inputs. Are the pools we will be sequencing composed of males and females, enabling QTL-seq or k-mer based mapping of SDR analysis? We have dedicated pipelines for both. If not, could you clarify how these markers should be identified? Please note that a chromosome-level assembly becomes increasingly important if this activity is required.

Answer: We do not require QTL mapping for sex-determining markers, as these markers will be included with the provided LD marker data. However, we will require you to validate the performance of the existing markers when integrating them with the newly generated HD marker set.

Trachinotus carolinus genome assembly FAU_TrCaro_2

- Trachinotus carolinus

Questions and Answers from 6/16/2026:

Question: Regarding the tissue samples from goats, sheep, and rodents: Will any of these contain parasites? If so, what specific protocols have been implemented to ensure the tissues are safe for handling?

Answer: We will not send tissue samples from any animal other than fish (specifically, Florida pompano), and these samples will not contain parasites.

Question: What is the biosafety level (BSL) associated with these tissue samples?

Answer: BSL1

Question: What specific type(s) of tissue will you be sending?

Answer: We will send fin clips collected from wild-caught and captive-bred Florida pompano.

Question: What is the expected amount or volume of tissue per sample?

Answer: The fin clips will be approximately 1-2 cm long, yielding >30 mg of tissue.

Question: You mentioned "providing digital gene expression signature profiles with full data analysis." Could you clarify if standard diƯerential gene expression analysis is suƯicient, or if you require any specific downstream analysis beyond that?

Answer: We do not require diƯerential gene expression analysis, as this is a WGS project focused on genome-wide SNP analysis for a high-density genomic selection tool.

Question: Will your project require strand-specific information?

Answer: No, we do not require strand-specific information.

Question: Do you plan to send the samples altogether in one batch? If they will be split up, how many batches should we expect, and how many samples will be in each?

Answer: The samples will be shipped together in a single batch.

Question: What type of RNA pre-processing is required for your project (e.g., poly-A selection or rRNA depletion)?

Answer: We do not require RNA pre-processing, as we intend to ship tissue samples for DNA extraction, whole-genome sequencing, and SNP panel development.

Questions and Answers from 6/15/2026:

Question: Will the fin clips be sent in any specific solution or in any specific condition (e.g. flash frozen, in RNAlater, etc.)?

Answer: Fin clips will be shipped in RNAlater cryovials on dry ice.

Question: Is each sample 1 fin clip? If not, please clarify.

Answer: Yes, each sample is one fin clip from an individual fish.

Question: What are the average sizes of the fin clips?

Answer: The fin clips are typically ~2 cm long.

Question: Do you need 20X coverage for each pool (5) or for each sample (5 x 10)?

Answer: We need 20X coverage for each sample.

Question: Will you ship your pools all in one batch? If not, please specify the number of batches and the number of pools per batch.

Answer: Yes, the samples will be shipped in a single batch.

Question: If known, is PCR-free library prep required?

Answer: Yes, we require PCR-free library preparation.

Question: When you mention that "scientists will assess the performance of SNP panels and determine the effectiveness before paying" does this mean scientists on your end will validate the panel performance, and we only need to perform WGS and panel development?

Answer: No, we will need you to perform WGS, panel development, and in-lab panel optimization + validation. We require a fully validated SNP panel ready for application in a selective breeding program.

Question: We noticed you mentioned the "SNP panel needs to be delivered 8 months after award and delivered to USDA Facility at 2001 South Rock Road, Fort Pierce, FL, 34945, USA." Can you confirm that you want a physical SNP panel (not just the design) delivered to this specific address?"

Answer: No, we will need the SNP panel design. This should include the raw and filtered data files (e.g., FASTQ, variant/genotype calls, FASTA sequences), detailed descriptions of the methods (for reproducible data analysis), and an interpretive report of the SNP results.