We have been working actively on the introductory book on genome assembly announced here - ‘An Easy-to-follow Introductory Book on NGS Assembly Algorithms’. This post is to inform you about the current status and our expected timeline.
The overall structure of the book is more or less finalized and stable. You can view the current table of contents at this link. It went through many revisions, but we believe the present form is close to final.
Status of various chapters -
A. Chapters 3, 4, 6 and 7 are borrowed from existing tutorials. They are going through some cleanup, but the contents remain similar to the tutorials and near complete.
B. ‘2. The Genome Assembly Problem’ - Apart from existing materials from the tutorials, we are adding a new section on fundamental limits of assembly. This section is unfinished, but will be completed by tomorrow.
C. 5. Experimental Considerations - We added this new chapter describing various sequencing technologies. It was not in the initial plan, but we later felt that a book on genome assembly algorithms should include some description of idiosyncrasies of different sequencing methods. We are working on this chapter.
D. 8. Faster, Better and Cheaper - This is another new addition covering a lot of cutting-edge algorithms, including various k-mer counting algorithms, efficient data structures for storing de Bruijn graphs, use of multiple k-mers to improve assembly quality, etc. The basic structure of this chapter is finalized, but writing some sections is taking time.
E. 9. In Depth Discussion of Three de Bruijn Graph-based Assemblers - This is another new addition not included in the tutorials, although we did some analysis of SOAPdenovo2 code elsewhere in the blog. We are continuing to work through the codes of SOAPdenovo2, SPAdes and Trinity to make this chapter as useful as possible.
Hands on exercises
We like to add some codes and exercises to each chapter. In fact, that was the main reason to get Pandora’s Toolbox for Bioinformatics ready so that readers of the book (expected to be relatively new to genome assembly) could find all materials at one place. We still have some work to do on the exercises and it will be done after the text is finalized.
We will have a draft version of the book ready for our readers by Feb 15th and will continue to improve parts of it after the first release. We like to release an early version so that all suggestions from readers can be incorporated to improve the text.
Please note that it is a ‘living’ electronic book. That means the publisher ensures that the readers will be able to access all later versions at no extra cost after they make their initial purchase. For example, if any new paper coming out in late 2015 makes some section of the book obsolete, in our method of publication we can easily update the book at that time to keep it always current. This ability to change the electronic text is a major advantage in a rapidly advancing field like NGS assembly.
We thank our readers for suggesting prices at the publisher’s website and feel very honored by those, who recommended prices all the way up to $100 !! The overall stats of readers’ suggestion are - (Average price - $27.03, Median Price - $20.00, Mode Price - $20.00).
Based on considering all numbers, we decided to make the initial price of the book - $14.95. It is considerably lower than what many readers suggested, lower than most technical books, and especially low for a technical book in a rapidly advancing field that will continue to be updated with the latest materials !! However, we chose the price for two reasons -
i) Our readers come from all over the world including India, China, Brazil, Philippines, and we like to make this book affordable to all of them.
ii) Since it is a living book and those making purchase will never have to pay extra to access the latest versions, we like to allow our regular blog readers take the most advantage of it through low initial price. Rewarding the regular blog readers is also beneficial for us, because they are the ones most likely to give feedback on various chapters.
If you have not done so, please sign up at the publisher’s website here so that we can let you know, as soon as the book is available. If you are not comfortable about leaving your email at their website, please email me at samanta_at_homolog.us and we will keep you posted.
Return policy - ‘happiness guarantee’
As you can see, we are doing a lot of work to make this book as useful as possible to everyone. If you are still unhappy, here is the best part !! The publisher has a happiness guarantee, which we really, really like. From their website -
We are proud of our return policy. We consider it a core Leanpub value.
Ruboss is proud to offer all readers The Leanpub Unconditional, No Risk, 100% Happiness Guarantee. Within 45 days of purchase you can get a 100% refund on any Leanpub purchase, unless you are abusing this refund policy. Readers can request a refund on their Leanpub dashboard pages. This is an honour system; there is no DRM or anti-circumvention or other copy-control system used. We believe that if we take the risk out of purchasing we will improve reader happiness, which should lead to more readers and thus more author happiness.
Abuse of the The Leanpub Unconditional, No Risk, 100% Happiness Guarantee leads to author unhappiness, so it will not be tolerated. Abusing the happiness guarantee means doing things like buying 3 bundles and 6 books and then immediately requesting refunds on all of them. This, and similar obviously exploitative behavior, goes against the spirit of the happiness guarantee. If we determine that a reader is abusing the happiness guarantee we will not refund the purchases, and we will inform the reader by email of that fact. If necessary, we will also inform PayPal of that fact, and provide PayPal with whatever information they require to determine if we are being fair in our judgment.