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Resource: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
...benchmarks in the more general problem of whole- alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three...
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Resource: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- Valerie A. Schneider,
- Tina Graves-Lindsay,
- Kerstin Howe,
- Nathan Bouk,
- Hsiu-Chuan Chen,
- Paul A. Kitts,
- Terence D. Murphy,
- Kim D. Pruitt,
- Françoise Thibaud-Nissen,
- Derek Albracht,
- Robert S. Fulton,
- Milinn Kremitzki,
- Vincent Magrini,
- Chris Markovic,
- Sean McGrath,
- Karyn Meltz Steinberg,
- Kate Auger,
- William Chow,
- Joanna Collins,
- Glenn Harden,
- Timothy Hubbard,
- Sarah Pelan,
- Jared T. Simpson,
- Glen Threadgold,
- James Torrance,
- Jonathan M. Wood,
- Laura Clarke,
- Sergey Koren,
- Matthew Boitano,
- Paul Peluso,
- Heng Li,
- Chen-Shan Chin,
- Adam M. Phillippy,
- Richard Durbin,
- Richard K. Wilson,
- Paul Flicek,
- Evan E. Eichler,
- and Deanna M. Church
Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
...relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex...
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Method: In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
- Andrew Adey,
- Jacob O. Kitzman,
- Joshua N. Burton,
- Riza Daza,
- Akash Kumar,
- Lena Christiansen,
- Mostafa Ronaghi,
- Sasan Amini,
- Kevin L. Gunderson,
- Frank J. Steemers,
- and Jay Shendure
Genome Res. December 2014 24: 2041-2049; Published in Advance October 19, 2014, doi:10.1101/gr.178319.114
...de novo assembly algorithms evaluated as part of the Assemblathon project (Earl et al. 2011; Bradnam et al. 2013). However, the data produced by CPT-seq is very different from that of mate-pair sequencing, consisting instead of sparse, shotgun representation of genomic DNA fragments that were...
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Resource: Efficient de novo assembly of large genomes using compressed data structures
- Jared T. Simpson and
- Richard Durbin
Genome Res. March 2012 22: 549-556; Published in Advance December 7, 2011, doi:10.1101/gr.126953.111
...established de novo assemblers: ABySS, Velvet, and SOAPdenovo. The performance of SGA has also been validated in a complementary comparison by a recent collaborative de novo assembly assessment project, the Assemblathon, organized by UC Santa Cruz and UC Davis. The organizers publically released simulated...
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Resource: GAGE: A critical evaluation of genome assemblies and assembly algorithms
- Steven L. Salzberg,
- Adam M. Phillippy,
- Aleksey Zimin,
- Daniela Puiu,
- Tanja Magoc,
- Sergey Koren,
- Todd J. Treangen,
- Michael C. Schatz,
- Arthur L. Delcher,
- Michael Roberts,
- Guillaume Marçais,
- Mihai Pop,
- and James A. Yorke
Genome Res. March 2012 22: 557-567; Published in Advance December 6, 2011, doi:10.1101/gr.131383.111
..., in contrast with other recent assembly evaluations such as the Assemblathon (Earl et al. 2011) in which the assembly parameters were not described. We also note that all of the data used in our evaluations were real sequence data from high-throughput sequencing machines, unlike the Assemblathon, which used...
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Method: Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
- T.S. Keshava Prasad,
- Ajeet Kumar Mohanty,
- Manish Kumar,
- Sreelakshmi K. Sreenivasamurthy,
- Gourav Dey,
- Raja Sekhar Nirujogi,
- Sneha M. Pinto,
- Anil K. Madugundu,
- Arun H. Patil,
- Jayshree Advani,
- Srikanth S. Manda,
- Manoj Kumar Gupta,
- Sutopa B. Dwivedi,
- Dhanashree S. Kelkar,
- Brantley Hall,
- Xiaofang Jiang,
- Ashley Peery,
- Pavithra Rajagopalan,
- Soujanya D. Yelamanchi,
- Hitendra S. Solanki,
- Remya Raja,
- Gajanan J. Sathe,
- Sandip Chavan,
- Renu Verma,
- Krishna M. Patel,
- Ankit P. Jain,
- Nazia Syed,
- Keshava K. Datta,
- Aafaque Ahmed Khan,
- Manjunath Dammalli,
- Savita Jayaram,
- Aneesha Radhakrishnan,
- Christopher J. Mitchell,
- Chan-Hyun Na,
- Nirbhay Kumar,
- Photini Sinnis,
- Igor V. Sharakhov,
- Charles Wang,
- Harsha Gowda,
- Zhijian Tu,
- Ashwani Kumar,
- and Akhilesh Pandey
Genome Res. January 2017 27: 133-144; Published in Advance November 15, 2016, doi:10.1101/gr.201368.115
...coverage of large s in a cost-effective fashion (Schatz et al. 2010; Salzberg et al. 2012). However, there are inherent challenges in assembly because of repetitive sequences, high GC content, and chimeric reads (Schatz et al. 2010). Indeed, substantial differences in assemblies have been reported when...

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