tag:blogger.com,1999:blog-36768584.post5806702908731594175..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Assembling a Review of a Review of AssemblingKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-36768584.post-90598244867046052432013-12-17T20:55:24.274-05:002013-12-17T20:55:24.274-05:00Mohamed:
Thank you for your response! I apologiz...Mohamed:<br /><br />Thank you for your response! I apologize that I meant to contact you via email & then failed to -- glad you found out anyway.<br /><br />I hope you found my comments helpful for any future endeavours -- I agree that trying to catch every last tool is a tall order.<br /><br />KeithKeith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-36040413878095983372013-12-17T20:37:57.220-05:002013-12-17T20:37:57.220-05:00Thank you very much for reviewing the review and t...Thank you very much for reviewing the review and thanks for Heng for his clarification. In fact I am the corresponding author of the review and I was about to comment about the timeframe that really made the difference. However, Heng, kindly, wrote it for me.<br /><br />Exactly as Heng said, we wrote this manuscript over a year ago (Nov. 2012- first draft) and it was submitted to PLoS Computational Biology early this year. The journal took quite long time to get it published. For instance, the paper was officially accepted Sep. 8th after revised submission in July, but it was published Dec. 12th. Unfortunately, PLoS CB only shows the publication date rather than showing the submission and acceptance dates. Otherwise, you could easily find that the omission is mainly because those tools were unpublished or were just published. Nevertheless, we missed some existing tools. Comprehensive surveying is really challenging in a rapidly growing area such as NGS and NGS assembly. <br /><br />Thanks again for taking time reading our paper and writing such long, yet useful, review. For Heng, thanks twice, for reviewing the review and reviewing the review of the review :) <br />Anonymoushttps://www.blogger.com/profile/00138921018028056566noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-77751909777999900332013-12-17T20:37:19.797-05:002013-12-17T20:37:19.797-05:00Thank you very much for reviewing the review and t...Thank you very much for reviewing the review and thanks for Heng for his clarification. In fact I am the corresponding author of the review and I was about to comment about the timeframe that really made the difference. However, Heng, kindly, wrote it for me.<br /><br />Exactly as Heng said, we wrote this manuscript over a year ago (Nov. 2012- first draft) and it was submitted to PLoS Computational Biology early this year. The journal took quite long time to get it published. For instance, the paper was officially accepted Sep. 8th after revised submission in July, but it was published Dec. 12th. Unfortunately, PLoS CB only shows the publication date rather than showing the submission and acceptance dates. Otherwise, you could easily find that the omission is mainly because those tools were unpublished or were just published. Nevertheless, we missed some existing tools. Comprehensive surveying is really challenging in a rapidly growing area such as NGS and NGS assembly. <br /><br />Thanks again for taking time reading our paper and writing such long, yet useful, review. For Heng, thanks twice, for reviewing the review and reviewing the review of the review :)Anonymoushttps://www.blogger.com/profile/00138921018028056566noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-240996155897429742013-12-17T12:31:02.734-05:002013-12-17T12:31:02.734-05:00Heng:
Thank you so much for the informative comme...Heng:<br /><br />Thank you so much for the informative comment! That does help fix the timeframe covered much better. Given that, I think some of the areas I hit are a bit unfair (the assessment area has really blossomed this year) & that explains some of the omitted assemblers (such as MaSurCa) but not some of the others (MIRA, Ray)<br /><br />I agree that having a format & the tools to drive it are really valuable; far too much time has been spent designing specs which never were used (indeed, I was once dragooned into such an effort)Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-10011032722331318592013-12-17T11:19:23.670-05:002013-12-17T11:19:23.670-05:00I am a referee for this review. The flaws in the r...I am a referee for this review. The flaws in the review largely reflect my ignorance in this area. Nonetheless, it should be noted that I got this review in April and the authors probably started the writeup in late 2012, when GAGE-B and this year's super stars like HGAP/SPAdes were unpublished yet. A few of tools you mentioned were just published back then or even have not been published today. While the authors could add more materials before it was accepted in July, they have done a job good enough for a publication.<br /><br />On the format, the key is to have an implementation along with the spec, such that the designers can know what are important in practice and that the assembler developers can feel the efforts in conforming to a generic format paid off. Few would use SAM/VCF nowadays if there were no samtools/vcftools in the first place.Heng Linoreply@blogger.com