Miseq DNA sequencing 2 x 300, per run

Added: Aug 22, 2017 10:39 am Modified: Aug 30, 2017 5:40 pmTrack Changes For a vendor to be considered for award all amendments must be signed and returned with their bid



This amendment is being issued to extend the close date from August, 28 12:00 Noon ET to September, 5 12:00 Noon ET.



Vendors have had many questions This amendment is being issued to

1. Extend the close date from August, 28 12:00 Noon ET to September, 5 12:00 Noon ET.

2. To Post answers to vendor questions



Can you please clarify the type of amplicons that will be submitted and the fragment size ; a) partial Illumina adapter ligated amplicons - which needs indexing and sequencing b) Illumina adapter and indexed amplicons- this would need only direct sequencing c) raw amplicons- which needs Illumina adapter and indexing (complete library preparation and sequencing)



Raw amplicons

2. Assuming raw amplicons will be submitted ¿ TruSeq kit as mentioned allows for only upto 96 indexes. It is mentioned upto 150 samples may be submitted for sequencing on one flow cell. Can you please clarify if the amplicons will have in-line barcodes and the samples will be pooled together? Please elaborate on the sample submission. If in-line barcodes will be present- will in-line barcode de-multiplexing be needed ? along with Illumina index de-multiplexing ? Please let us know.

In line barcodes are present, and don¿t need de-multiplexing

3. Can you please comment on the number of batches, samples per batch and the timeline of the sample submission. ¿ we would need this information to accurately provide you with a quote.

Batches are up to 4 in the course on contract, with up to 6 runs, some some batches may have 2-3 runs. Anticipate first batch in fall of 2017 and the final batch in late summer of 2018. Timing of intermediate batchesis unknown.



"1) What actually is being provided to the vendor? Is it extracted DNA? Amplified DNA, but DNA that is not indexed? DNA that is amplified and indexed? It is unclear, because it sounds like the DNA has already been amplified and indexed, but the offeror is stating that library prep is needed. Library prep is only needed if the DNA has not been amplified and indexed (or at least indexed).



2) I am not sure that the quality control requirements are reasonable. We have used the v3 2x300 kits before. There is no chance of getting 70% of the bases >Q30. These kits just don¿t work well on the Miseq¿s. Also you won¿t get 40M reads passing filter for an individual run. Also note that many of your amplicons will exceed 600 bp which makes getting merged reads impossible for those. You might want to adjust your requirements here, or switch to a 2x250 kit, which we have found works much better.'



Using a dual-index sequencing strategy GLKN will produce PCR DNA amplicons from filtered water and tissues using metagenomics primer sets, combined with an Illumina adaptor, 8 bp index sequence, 10 bp pad sequence and 2 bp linker sequence. Amplicon length of the provided DNA fragments will be 400-650 bp. In the provided samples, the amplicons will be barcoded and pooled in equal concentration for sequencing.



Yet, the next statement highlighted below indicates that the vendor is expected to prepare libraries using the Illumina TruSeq Kit, which would have already been accomplished per the above statement.

The vendor will perform library preparation using the Illumina TruSeq Kits, or comparable library chemistry, that allows 96 indexes and give comparable output quality to TruSeq.



The question is: are the libraries indeed premade and ready to run, or is the vendor expected to prepare the libraries from the amplicon material?"



Vendor must prepare library from `raw¿ amplicons, that will have a barcode index incorporated. No Illumina indexes are in raw amplicons.



What should be included in Technical capability?

Examples of problems in projects like this and resolution, Degrees held by staff.



For a vendor to be considered for award all amendments must be signed and returned with their bid

Added: Aug 22, 2017 10:39 am Modified: Aug 24, 2017 1:05 pmTrack Changes This amendment is being issued to extend the close date from August, 28 12:00 Noon ET to September, 1 12:00 Noon ET.

Vendors have had many questions; the scientist who will answer these is out of office until August, 28. A second amendment addressing the questions will be issued once the scientist is back and resolves them.

For a vendor to be considered for award all amendments must be signed and returned with their bid

Added: Aug 22, 2017 10:39 am THIS IS A NOTICE OF INTENT FOR REQUEST FOR QUOTE. This is a combined synopsis/solicitation for a commercial item being procured in accordance with the format in Subpart 12.6, and supplemented with additional information as included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. The National Park Service intends to solicit quotes for a service of DNA Sequencing Services Greatlakes Network Wisonsin

This is the solicitation number P17PS2671 and is issued as a request for quote (RFQ). This requirement is a 100% total small business set-aside. The associated NAICS code is 541711. The small business size standard is 1000 employees. Provisions and clauses are, incorporated in this solicitation document. Anticipated Award Date: on or before 09/01/2017 with an effective date of 09/01/2017.

To be considered for award your company must obtain a Dun and Bradstreet Number (DUNs). You may obtain this number free of charge at 1(866)705-5711. Your company must also be registered in the System for Award Management (SAM) with the appropriate NAICS code for this solicitation (located in block 10 on the form), web site: https://www.sam.gov .

If you have any registration questions, please call 866-606-8220. If you need assistance with registration or updating SAM please contact the Procurement Technical Assistance Center nearest you at (615) 268-6644 or website: http://www.aptac-us.org/new/Govt_Contracting/find.php.

GENERAL DESCRIPTION OF STATEMENT OF WORK

Independently, and not as an agent of the Government, the Contractor shall furnish all labor, materials, and equipment necessary to provide DNA Sequencing Services for Great Lakes network

Quotes are due at 12:00 Noon PM ET, 28 August, 2017. Offers may be submitted by email to thomas_hershberger@nps.gov. Questions regarding this solicitation will only be accepted until 12:00 PM ET, 25 August, 2017.



OFFERS SHALL INCLUDE THE FOLLOWING:



1. Price quotes for line items referenced in the solicitation number provided above:



CLIN Structure: listed on the SF 1449 ¿ the bid schedule and the line items on the SF 1449 must be completed, the following CLIN structure does not have to be completed.



0010 ¿ DNA Sequencing Service





Unit Price $__________ Total Cost (includes discounts) $__________





2. Remittance address and DUNS number













3. If the contractor is claiming an exception or change to the SAM then the contractor must supply FAR Clause 52.213-3 in its entirety



4. Letter of capability





5. Technical Questionnaire (see attachment)



6. Past Performance Questionnaire (see attachment)