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