tag:blogger.com,1999:blog-36768584.post3336517829505319112..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Chromosome-Scale Scaffolds And The State of Genome AssemblyKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-36768584.post-68329304660508672672017-04-12T08:14:00.822-04:002017-04-12T08:14:00.822-04:00Hi Olga,
these costs can only be matched if you&#...Hi Olga,<br /><br />these costs can only be matched if you're in academia, have extensive lab knowledge and don't account for the time (and salary) a bioinformatician has to spend performing the analysis. Outside academia and when you actually have to pay the full cost for DNA extraction, sequencing, HiC scaffolding etc. it's about 4x as much.<br /><br />Best,<br />Chris Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-50730693492656278232017-04-02T15:39:59.020-04:002017-04-02T15:39:59.020-04:00Hey Keith,
Thank you so much for writing such a t...Hey Keith,<br /><br />Thank you so much for writing such a thoughtful post about our paper!<br /><br />I did want to clarify one point. In a few places you say that the Hi-C sequencing costs $10K. Actually, the $10K value we report is the total amount for a de novo human genome, including both the contigs (which are the lion's share of the cost: 60X coverage, Illumina PE 250bp) and the Hi-C data used for scaffolding (<7X Illumina PE101bp). The Hi-C cost alone - including library prep and labor - is less than $1K.<br /><br />Thus the contigs are the expensive part, and when contigs are already available (whether generated using Illumina, PacBio, or any other method), the costs can be much lower! In the case of the Aedes genome, for which contigs were available from the 2007 Science publication (Nene et al.), we used only $1K worth of Hi-C sequence for the scaffolding. Similarly, Culex was also about $1K worth of sequencing.<br /><br />These costs are broken down in supplemental table S12. They can vary based on factors like contig length, genome length, and genome repeat structure, and will drop as the cost of short reads continues to fall.<br /><br />Best,<br />OlgaAnonymousnoreply@blogger.com