Tenders are invited in the department

Post date: Mar 10, 2018 9:36:8 AM

No. DCB/ADMIN/ 402 /17-18 08/03/2018

Tender Notice

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

1. Each bidder shall submit only one Tender

2. Fax/email bids shall not be accepted.

3. Late/Delayed and tenders shall not be opened.

4. Wrongly referenced / enclosed Tenders and Unsigned (wherever signature required) bids will be

rejected summarily

5. The companies participating should provide the Installation certificate for PacBio in their facility in

India

6. The cost should be mentioned separately for sequencing using different platforms and

bioinformatics analysis

7. Payment conditions: 100% payment on receipt of the results as per specifications.

8. The sample should not be sent outside India for sequencing.

9. 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, transcriptome sequencing and de novo assembly using next generation sequencing platforms for

undertaking the sequencing, assembly and annotation of the whole genome and transcriptome of Evolvulus

alsinoides.

The details of the plant species and sequencing specifications are given below.

Details of the plant species

Common name - Vishnukranthi

Scientific Name - Evolvulus alsinoides

Chromosome number - 2n= 26

Genome size (haploid) - ~ 1 GB

Specifications for sequencing

1. Whole Genome Sequencing and analysis of Evolvulus alsinoides using PAC Bio RS II/Sequel and Illumina HiSeq 2500 platforms

2. 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.

3. De novo assembly of the comprehensive sequence data set with a minimum of 80% genome coverage.

4. Primary Bioinformatics analysis should include Base Calling, Filtering, Trimming

5. Secondary Bioinformatics analysis should include Error correction and Denovo Assembly using CLR reads, Functional Annotation of the reads based on our pipeline.

6. 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.

7. De Novo Transcriptome Sequencing, assembly and Bioinformatics Analysis of Evolvulus alsinoides samples on Illumina HiSeq 2500/4000 Platform for 4 samples.

8. Primary Bioinformatics analysis should include Base Calling, Filtering, QC, Trimming, contamination removal.

9. Secondary Bioinformatics analysis should include Error correction, Denovo Assembly and Mapping of Transcriptome to the Hybrid assembled Genome

The following information also should be provided in the Tender.

a. Proposed sequencing and assembly strategies in detail for Evolvulus alsinoides

b. Type of sequencing platform (s) including software/ programme modules to be used.

c. Modal read lengths for different platforms

d. Depth of sequencing

e. Details of all bioinformatics services to be provided

All interested service providers are requested to send their Tender in sealed envelope superscribing

“Tender No. DCB/ADMIN/402/17-18–dt 08/03/2018” for Next Generation Sequencing Work” to “The

Head, Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom,

Trivandrum, Kerala, India- 695581” on or before 5pm on 30-03- 2018. The received Tenders will be

opened on the next working day at 10am.

Head

Department of Computational Biology and Bioinformatics