Quotations Invited for NGS service

Post date: Nov 30, 2017 10:26:22 AM

Tender Notice - I

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 sequencing and de novo assembly using next generation sequencing platforms for undertaking the sequencing and assembly of the whole genome of Phytophthora capsici

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

Details of the species

Scientific Name - Phytophthora capsici

Host plant – Black pepper

Genome size - ~ 63 Mb

Specifications for sequencing

1. Whole Genome Sequencing and analysis of Phytophthora capsici 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 illumina 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.

Deliverables

1. Raw reads

2. Bioinformatics Analysis: Detailed Assembly Statistics of estimated genome size, Genomic G + C content, genome coverage, list of aligned reads, Number of assembled scaffolds, Number of scaffolds > 20 kb in length, Scaffold N50, Scaffold L50, Number of contigs, Number of contigs > 20 kb in length, Number of contigs > 2 kb in length, Scaffolded contig N50, Scaffolded contig L50.

● Error correction and re-analysis

● k-mer optimization

● Assembly Validation

3. Details of Gene prediction statistics with above said parameters

● Total number of genes

● Maximal coding sequence length

● Minimal coding sequence length

● Median coding sequence length

● Maximal intron length

● Minimal intron length

● Number of single exon genes

● Gene Ontology and KEGG IDs

● Gene Model prediction and publicly available EST mapping during assembly

● Repetitive sequence finding

The following information also should be provided in the Tender.

1. Proposed sequencing and assembly strategies in detail for Phytophthora capsici

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

3. Modal read lengths for different platforms

4. Depth of sequencing

5. Details of all bioinformatics services to be provided

All interested vendors are requested to send their Tender in sealed envelope superscribing “Tender No. DCB/Ann.Plan.F/277/17-18 – dated 30/11/2017 for Next Generation Sequencing Work” to “The Head, Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom, Trivandrum, Kerala- 695581” on or before 5PM on 15-12-2017. The received Tenders will be opened on the next working day at 10AM.

Tender Notice- II

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, GST, 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 tenders shall not be opened.

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

5. The cost should be inclusive of sequencing and bioinformatics analysis.

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

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

8. Delivery: To be made available to this Institute in soft copies and hard disc.

Annexure

Tenders are invited from firms providing sequencing services with proven track record of small RNA sequencing using next generation sequencing platforms for undertaking the miRNA sequencing and bioinformatics analysis of the Human cells using Illumina Hiseq 2500.

The details of the sequencing and specifications are given below.

Details of the Sequencing

Small RNA sequencing, specifically miRNA sequencing of Human cells.

Test sample: 2 (sequencing to be done in triplicates) (2× 3 = 6 samples)

Control sample: 1 (sequencing to be done in triplicates) (1× 3 = 3 samples)

Total No: of samples: 9

Specifications for sequencing

1. Small RNA Sequencing and analysis of Human cells using Illumina HiSeq 2500 platform.

2. Library – 1 × 50 bp Illumina reads (× 9 samples)

3. Data required: 20 million reads (× 9 samples)

4. Primary Bioinformatics analysis should include Base Calling, Filtering, QC analysis, adapter trimming, and contamination removal.

5. Secondary Bioinformatics analysis should include mapping the sequenced miRNAs to miRBase & identifying known/ novel miRNAs, prediction of miRNA targets, differential expression analysis and functional annotation of differentially expressed miRNAs and their target genes.

Data analysis and Deliverables

1. Raw reads

2. Quality check &Filter: The read quality of the fastq files need to be assessed and necessary quality filters such as removal of low quality reads, low quality read trimming should be performed. A quality check report has be provided.

3. Adapter trimming: The adapter sequences part of the fastq sequences need to be trimmed. A summary of adapter trimming including read length summary after trimming need to be provided.

4. Contamination removal: The sequences similar to rRNA, tRNA, snoRNA, snRNA and other non-coding RNAs need to be filtered out for further analysis. A summary report of contamination removal and distribution of reads into various non-coding RNA class should be provided.

5. Alignment to reference miRNA/Identification of conserved miRNA: If the reference precursor miRNA sequences are available (mainly at miRBase database) the reads need to be aligned to it. Otherwise the sequences should be aligned to the species closest to it and for which the reference precursor miRNA sequences are available. Total number of reads falling in each miRNA class should be provided.

6. Prediction of novel miRNAs: Based on the sequence secondary structure around the miRNA sequence and position of mature miRNA reads on the secondary structure, novel miRNAs need to be predicted.

7. Prediction of miRNA targets: The miRNA target genes/transcripts need to be identified. Also functional annotation of the target genes should be provided based on the gene annotation available in public domain.

8. Differential expression analysis: Differential expression analysis need to be performed and a list of differentially expressed miRNAs will have to be identified from the samples. Also, functional annotation of the differentially expressed miRNAs and their target genes should be provided.

The following information also should be provided in the Tender:

1. Proposed small RNA sequencing strategies in detail for the human cell lines

2. Type of sequencing platform including software/ programme modules to be used

3. Depth of sequencing

4. Details of all bioinformatics services to be provided

All interested vendors are requested to send their Tender in sealed envelope superscribing “Tender No. DCB/Ann.Plan.F/277/17-18 – dated 30/11/2017 for Next Generation Sequencing Work” to “The Head, Department of Computational Biology and Bioinformatics, University of Kerala, Kariavattom, Trivandrum, Kerala- 695581” on or before 5PM on 15-12-2017. The received Tenders will be opened on the next working day at 10AM.