Tender Notice
Post date: Mar 27, 2017 11:0:26 AM
Sub : Tenders invited for Next Generation Sequencing (NGS) service
Competitive Tenders are invited from service providers for carrying out Next Generation Sequencing work as shown in Annexure. Tenders should specifically show the charges, taxes, forwarding charges and terms of delivery separately. Evaluation will be based on total amount. Validity of the offer and the time required for effecting the sequencing work after placing the order should also be mentioned in the Tender.
Successful bidder has to complete the work within the stipulated time failing which the order will be treated as cancelled without any further intimation. You are requested to quote the reference number and date of this letter in all your correspondence.
Terms and Conditions
Each bidder shall submit only one Tender
Fax/email bids shall not be accepted.
Late/Delayed and tenders shall not be opened.
Wrongly referenced / enclosed Tenders and Unsigned (wherever signature required) bids will be rejected summarily
The companies participating should provide the Installation certificate for PacBio in their facility in India
The cost should be mentioned separately for sequencing using different platforms and bioinformatics analysis
Payment conditions: 100% payment on receipt of the results as per specifications.
The sample should not be sent outside India for sequencing.
Delivery: To be made available to this Institute in soft copies and hard disc.
Annexure
Tenders are invited from firms providing DNA sequencing services with proven track record of whole genome sequencing and de novo assembly using next generation sequencing platforms for undertaking the sequencing and assembly of the whole genome of Trichopus Zeylanicus.
The details of the plant species and sequencing specifications are given below.
Details of the plant species
Common name - Arogyapacha
Scientific Name - Trichopus zeylanicus
Chromosome number - 2n= 28
Genome size (haploid) - ~ 1 Gb
Specifications for sequencing
Whole Genome Sequencing and analysis of Trichopus zeylanicus using PAC Bio RS II/Sequel and Illumina HiSeq 2500 platforms
Library – Insert range for Illumina is 200-800 bp. PE library should be sequenced using 2x100bp PE sequencing (100x). Total Coverage for illumine data should be 100x per Sample. The insert size for Pacbio sequencing should be around 20 kb and minimum read length should be 8 kb. Total Coverage for Pacbio data should be 20x per Sample.
De novo assembly of the comprehensive sequence data set with a minimum of 80% genome coverage.
Primary Bioinformatics analysis should include Base Calling, Filtering, Trimming
Secondary Bioinformatics analysis should include Error correction and Denovo Assembly using CLR reads.
The final report should contains Statistics of raw reads, Raw data QC, Statistics of clean and filtered reads, Statistics after error correction, Denovo assembly and Hybrid assembly, Scaffolding and gap closure.Distribution of reads throughout the genome to be provided.
The following information also should be provided in the Tender.
Proposed sequencing and assembly strategies in detail for Trichopus Zeylanicus
Type of sequencing platform (s) including software/ programme modules to be used.
Modal read lengths for different platforms
Depth of sequencing
Details of all bioinformatics services to be provided
All interested vendors are requested to send their Tender in sealed envelope superscribing “Tender No. No. DCB/SIUCEB/445/16-17 - dt27/03/2017” for Next Generation Sequencing Work” to “ The Director, SIUCEB, Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom, Trivandrum, Kerala, India- 695581” on or before 5pm on 15-04-2017. The received Tenders will be opened on the next working day at 10am.