Can someone tell a price estimate (EUR) how much it would cost to sequence a plant genome with an approx size of 1200 Mbp? Platforms: illumina/PacBio/454.
There are several factors that need to be be considered such as polyploidy or rececent whole genome duplications, heterozygosity and repeat content. For the most simple case scenario, where your plant is diploid and highly homozygous, the most common approach (at this point) is to create a base assembly with Illumina and then improve the scaffolding and fill the gaps with PacBio.
For the Illumina assembly is recommended at least 100X of pair ends (PE) to build the contigs and then complement that with mate pair (MP) libraries with different insert sizes for the scaffolding (e.g. 3Kb, 5Kb, 10Kb and 20Kb) each of then with at least 10-15X. For a 1.2 Gb genome, with Illumina HiSeq2500 (yielding 35Gb/lane) and approx. $2,500 per 2x100 lane, $300 per library prep for PE and $800 for MP, the cost could be around $18,500 (4 lanes PE, 2 lanes MP with 2 lib. per lane).
PacBio is more expensive, but combining it with the Illumina assembly and using it just to finish the genome 5-10X could be okay. I am not sure about the current prices, but it could be around ~$20,000.
To do a 454 sequecing at this point is very expensive if you compare with the Illumina/PacBio approach.
I hope this helps,
That offcourse depends on how 'deeply' you would like to sequence it. For human whole genome sequencing we are close to the 'mythical' 1000 dollar genome. Since the plant genome you speak of is about 1.8x smaller than the human genome, you can make a guess.
I have no experience with plant genomics, however, some with human whole genome sequencing.
There are several factors that need to be be considered such as polyploidy or rececent whole genome duplications, heterozygosity and repeat content. For the most simple case scenario, where your plant is diploid and highly homozygous, the most common approach (at this point) is to create a base assembly with Illumina and then improve the scaffolding and fill the gaps with PacBio.
For the Illumina assembly is recommended at least 100X of pair ends (PE) to build the contigs and then complement that with mate pair (MP) libraries with different insert sizes for the scaffolding (e.g. 3Kb, 5Kb, 10Kb and 20Kb) each of then with at least 10-15X. For a 1.2 Gb genome, with Illumina HiSeq2500 (yielding 35Gb/lane) and approx. $2,500 per 2x100 lane, $300 per library prep for PE and $800 for MP, the cost could be around $18,500 (4 lanes PE, 2 lanes MP with 2 lib. per lane).
PacBio is more expensive, but combining it with the Illumina assembly and using it just to finish the genome 5-10X could be okay. I am not sure about the current prices, but it could be around ~$20,000.
To do a 454 sequecing at this point is very expensive if you compare with the Illumina/PacBio approach.
I hope this helps,
Hi Peter,
The National Human Genome Research Institute (NHGRI), from NIH, has been tracking the cost (estimated cost) of sequencing a genome. See attached figure (this is based on a genome size of 3,000 Mb). For details, please see their website for concise explanation of how to estimate the cost of sequencing a genome.
http://www.genome.gov/sequencingcosts/
The initial plunge off of a near Moore's Law path is impressive enough but its longevity was clearly short. Perhaps another drop is in the offing.
Depend on coverage you are expecting. It will be nice if you used two systems to have confidence. Dr. Aureliano Bombarely has given you nice calculations and hope it will work for you.
It would be beneficial (for me at least) to know a few of the assumptions made by those who commented earlier. For instance, I would like to know the length of the average sequenced contig. Generally, I see the ordering of contigs into a complete genome to be rather a simple problem; for all but highly repetitious contigs, enough unique subsequences can be found to give alignment without great difficulty, if the contigs are of lengths of at least 300 base pairs.
Wouter De Coster your comparison doesn't really stand, as for humans we have developed over the years multiple resources (like a genome assembly), so the $1000 dollar genome is to sequence an individuals (human) genome, while having already a very good genome assembly available that has been thoroughly validated and studied (although much still needs to be discovered/understood about it).
For a de novo genome assembly for a plant with no available genomic resources a lot of factors are involved. E.g., do you have a closely related species or linkage map you could use for anchoring of scaffolds? and, as Aureliano mentioned in his great answer, is there duplication? How common are repetitive elements, etc.
I've been discussing this a bit with other researchers sequencing prawn and oysters genomes at our University, and the cost can vary a lot but I would account for some 30-40.000 euros to achieve a complete good quality draft with not too many scaffolds. Then once again, how complex your genome is puts huge confidence intervals on my not-very-accurate-to-start-with estimate
This article mentions many of the topics touched upon, as well as summarising costs for some major workflows:
https://www.nature.com/articles/nrmicro2850#ref2
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