Feedback and analysis of the Assemblathon 2 pre-print and published paper
There has already been some discussion of the pre-print of the Assemblathon 2 manuscript. Although a pre-print is not the same thing as a peer-reviewed, accepted paper — I don’t want us to get too ahead of ourselves! — I thought it useful to start collecting together some of the online commentaries:
- Homolog.us blog post 1: highlights a few conclusions from the paper
- Homolog.us blog post 2: delves into the results, and attempts to estimate some of the costs of genome assembly. Assemblathon co-author Sébastien Boisvert adds some useful comments.
- Haldane’s Sieve post: an invited blog post by lead author Keith Bradnam, that summarizes what the Assemblathons are all about by way of a pizza-themed analogy
- Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons: this is not a blog post, but a recently published paper that evaluates some of the Assemblathon 2 data
- Thoughts on the Assemblathon 2 paper: by C. Titus Brown (a reviewer of the manuscript)
- Homolog.us blog post 3: reactions to the previous post by C. Titus Brown
- Assemblathon 2 review, round 1, parts thereof: a concise version of C. Titus Brown’s formal manuscript review (minus the specific suggestions)
- On assembly uncertainty (inspired by the Assemblathon 2 debate): blog post by Lex Nederbragt in response to post by C. Titus Brown
Since the paper was officially published (22nd July, 2013) there has been several commentaries about the paper and about the open nature of the writing and peer review process:
- Genome assembly contest prompts soul-searching: commentary on the official publication of the paper on Nature’s News blog
- Homolog.us blog post 4: Two Important Papers Published – Assemblathon and First Genome using Moleculo
- Genome assembly in the spotlight: press release by BioMed Central
- Unusual ‘meta’ peer review: A video of GigaScience Editor-in-chief, Laurie Goodman, discussing the open nature of the peer-review process.
- Ultra-Open Peer Review: A blog post by Laurie Goodman writing about the issues discussed in the video of the previous link.
- Genome assembly in the spotlight: a blog post that expands on the press release (mentioned above).
- Writing the Assemblathon 2 paper, an experiment in openness: another post from this blog about the whole experience of writing, and reviewing, the paper.
- Mining Altmetric Data To Discover What Types Of Research Article Get The Most Social Media Engagement: a personal blog post by me (Keith Bradnam) about the impact of both Assemblathon papers as assessed by chatter on social media sites.
- Assemblathon 2 Results Highlight Efficacies, Challenges of De Novo Genome Assembly Algorithms: a long piece by Uduak Grace Thomas at GenomeWeb that discusses the paper and interviews me (Keith Bradnam) and one of the reviewers (Mick Watson). A (free) account is needed with GenomeWeb to view this article.
- Exploring Genome Characteristics and Sequence Quality Without a Reference: a new pre-print in arxiv.org by Jared Simpson. The Acknowledgements include the following: The project was motivated in part by online discussion of the Assemblathon2 paper centered on a blog post by Titus Brown.
- Keith Bradnam on Assemblathon 2: putting genome assembly tools to the test: a Q&A interview with Biome, the magazine of BioMed Central. The extended version of this interview (director’s edition?) is also available.
- Thoughts on Assemblathon 3: another blog post on this site that looks back at Assemblathon 2 to see what lessons could be applied to any future Assemblathon 3.
- Uncertainties in Assembly: Communicating and Managing the Truth About Our Data: An interview with C. Titus Brown by Bio-IT World that discusses the Assemblathon 2 paper.
- End of Short-Read Era? – (Part I): Another homolog.us blog post that briefly discusses reasons why there is no need for an Assemblathon 3
- Genome researchers find software used to piece together genetic codes are not reliable - Could the crackers of genomes be doing it all wrong?: A piece for MyScienceWork.com
- In need of an upgrade - A Nature Biotechnology editorial which discusses the results of Assemblathon 2 in the wider context of the accessibility and documentation of software associated with papers.
Remember, the Assemblathon twitter account has also tweeted about these pieces, as well as many other articles relating to genome assembly.
