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 GenerationRemoval Of Ribosomal Rna Using Ribozero Or Equivalent Technology . 2 X 150 Base Pair Paired End Reads24Gb Data Per Sample With Q30 Of 90% Per Sample Is Required . , Work Includes M-Rna Isolation And Data GenerationRemoval Of Ribosomal Rna Using Ribozero Or Equivalent Technology . 2 X 150 Base Pair Paired End Reads12 Gb Data Per Sample With Q30 Of 90% Per Sample Is Required . , Ngs Transcriptome Data ( Microrna ) : , Work Includes Micro Rna Isolation And Data Generation60 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 Enzyme2 . Dna Should Be Treated For Bisulfite Conversion For Individual Sample3 . Dna Bisulfite Library Should Be Prepared For Each Sample4 . 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 Nucleotides2 . Rates To Be Quoted Per Sample Separately For Two Read Lengths3 . Separate Rates To Be Given For Samples With Purification And Without Purification4 . Data To Be Provided As Chromas File/Ab1 Files , Raw Sequence5 . Samples To Be Picked From Nbagr By The Vendor6 . 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 Sequencer2 . Minimum Read Length 600 To 900 Nucleotides And 900 To 1200 Nucleotides3 . Rates To Be Quoted Per Sample Separately For Two Read Lengths4 . Data To Be Provided As Chromas File/Ab1 Files , Raw Sequence5 . Samples To Be Picked From Nbagr By The Vendor6 . 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
