Rate Contract for Outsourcing of Sequencing Services at ICAR-NBAGR, Karnal

PAC Bio Data Generration:

10 Kb CCS library preparation and one SMART cell with minimum of 10 GB data of size greater than 10 Kb.

20 Kb CCS library preparation and one SMART cell with minimum of 10 GB Hi Fi data of size greater than 15 Kb.

30 Kb CLR library preparation and one SMRT cell with minimum of 10 GB data of size greater than 18 Kb.

10X Genomics

10X genomics supernova assembly with isolation of high molecular weight DNA with size of 100Kb, QC library preparation from the DNA of 10 X chromium library of size 50-100 Kb molecule length. Sequencing on Illumina Platform with 360GB linked reads data

Optical Mapping:

Optical Mapping and Super Scaffolding, isolation of DNA with >300Kb molecule length, QC by PFGE, Nicking and labeling with DLS system using DLEI enzyme data generation of 700-800GB output per flow cell

Hi C Validation and Super Scaffolding :

Isolation of High Molecular weight DNA of size >300Kb, QC with PFGE, HiC Library preparation using two different methods (eg; Arima, Dovetail, phase genomic etc.), > 30 Mb Cross Links. 100 X coverage per HiC library with a total of 720GB data. Approximate required coverage shall be approximate >200 X. Validation of Hi C Data, Manual curation and super scaffolding at chromosome level to cover atleast 90% of Genome in chromosome level scaffolds.

PAC Bio ISOseq Sequencing:

Size of the Library : 500 to 2 Kb, 2-5Kb and 5-10Kb The work includes isolation of RNA from the tissues, Library preparation and data generation. 24GB high quality subread data per library.

NGS Transcriptome Data:

Work Includes m-RNA isolation and data generation Removal of Ribosomal RNA using Ribozero or equivalent technology. 2 X 150 base pair paired end reads 24GB data per sample with Q30 of 90% per sample is required.

Work Includes m-RNA isolation and data generation Removal of Ribosomal RNA using Ribozero or equivalent technology. 2 X 150 base pair paired end reads 12 GB data per sample with Q30 of 90% per sample is required.

NGS Transcriptome Data (MicroRNA) :

Work Includes micro RNA isolation and data generation 60 million reads of 1X50bp with Q30 of 80%

Custom Genotyping Designs for Microarry Genotyping:

Custom Genotyping Designs for Microarry Genotyping for two Species: >90,000 SNPs---SNP Chip as per the specifications mentioned in tender document Annexture-1 Page No. 22-23

Custom Genotyping Designs for Microarry Genotyping

Custom Genotyping Designs for Microarry Genotyping for two Species: >500,000(500K)SNPs---High Definition Chip as per the specifications mentioned in tender document Annexture-1 Page No.23

Whole Genome Reduced Representation Bisulfite Sequencing (RRBS):

1. Digestion with restriction Enzyme 2. DNA should be treated for Bisulfite conversion for individual sample 3. DNA Bisulfite library should be prepared for each sample 4. Sequencing should be done using 150 paired end chemistry to generate 9-10 GB data/sample on illumine or other related platform. Rawdata Statistics, QC processed reads to be provided in a separate ard disk as per the specifications mentioned in tender document Annexture-1 Page No.23

Genome Sequencing using Pacbio Sequel :

Swamp buffalo genome sequencing specification: A. Genome Sequencing of 1 sample; Genome size ~2.9 GB (Blood samples will be provided: DNA isolation to be carried out in the firm; Total Samples: 1) as per the specifications mentioned in tender document Annexture-1 Page No. 23

Genome sequencing using illumina Hiseq :

Genome sequencing ; Genome size ~2.9 GB (Blood samples will be provided: DNA isolation to be carried out in the firm; Total Samples: 1) as per the specifications mentioned in tender document Annexture-1 Page No. 24

ddRAD sequencing of Cattle and Buffaloes samples :

ddRAD sequencing of Cattle and Buffaloes as per the specifications mentioned in tender document Annexture-1 Page No. 24

Whole genome resquencing :

Whole genome resquencing of cattle samples with 10X coverage

Microsatellite Genotyping (PCR Multiplex) :

Microsatellite Genotyping (PCR Multiplex) Plates ready to run on sequencer @ per Plate

Microsatellite Genotyping :

Microsatellite Genotyping of 96 DNA samples with 25 primers (DNA, Fluorescent dye labeled primers and multiplexing details will be provided @ rate per well of Multiplexed Plate

Dideoxy Sanger sequencing PCR products/clones :

1. Minimum read length 600 to 900 nucleotides and 900 to 1200 nucleotides 2. Rates to be quoted per sample separately for two read lengths 3. Separate rates to be given for samples with purification and without purification 4. Data to be provided as Chromas file/AB1 files, raw sequence 5. Samples to be picked from NBAGR by the vendor 6. Reaction failures to be repeated free of cost. 7. Results should be provided within a week after receiving the samples, online/email

Sanger sequencing ready to run samples :

1. Ready to run ABI BDT Cycle Sequencing Kit reaction samples will be provided after purification step in Hi-Di formamide for directly running on ABI sequencer 2. Minimum read length 600 to 900 nucleotides and 900 to 1200 nucleotides 3. Rates to be quoted per sample separately for two read lengths 4. Data to be provided as Chromas file/AB1 files, raw sequence 5. Samples to be picked from NBAGR by the vendor 6. Run failures to be repeated free of cost. 7. Results should be provided within a week after receiving the samples, online/email.

SNP Genotyping :

Custom SNP Genotyping of 16SNPs of multiples thereof and 100 samples. Cost of 16 SNPs to be provided

Nucleome Informatics Pvt Ltd

magnus enterprise

Clevergene Biocorp Pvt Ltd

Bencos Research Solutions Private Limited

Agrigenome Labs Pvt Ltd

Bionivid Technology Pvt Ltd

Clevergene Biocorp Pvt Ltd

NxGenBio Life Sciences

Bencos Research Solutions Private Limited

Nucleome Informatics Pvt Ltd