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Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
- Wenjuan Yu,
- Haohui Luo,
- Jinbao Yang,
- Shengchen Zhang,
- Heling Jiang,
- Xianjia Zhao,
- Xingqi Hui,
- Da Sun,
- Liang Li,
- Xiu-qing Wei,
- Stefano Lonardi,
- and Weihua Pan
Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
..., and accuracy of 11 assemblers. We hope that our data sets (which include HiFi reads for a newly sequenced tetraploid, the wax apple) will become a benchmark for future assembler development. Five novel k-mer-based criteria were introduced to help assess assemblies’ quality.Our concluding remarks are in order...
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RESEARCH: Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
- Brent Ewing and
- Phil Green
Genome Res. March 1, 1998 8: 186-194; doi:10.1101/gr.8.3.186
.... Genome Res. 6: 80–91. Ewing, B., L. Hillier, M. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. (this issue). Giddings, M.C., R.L. Brumley Jr., M. Haker, and L.M. Smith. 1993. An adaptive, object oriented strategy for base calling...
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Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
- Dent Earl,
- Keith Bradnam,
- John St. John,
- Aaron Darling,
- Dawei Lin,
- Joseph Fass,
- Hung On Ken Yu,
- Vince Buffalo,
- Daniel R. Zerbino,
- Mark Diekhans,
- Ngan Nguyen,
- Pramila Nuwantha Ariyaratne,
- Wing-Kin Sung,
- Zemin Ning,
- Matthias Haimel,
- Jared T. Simpson,
- Nuno A. Fonseca,
- İnanç Birol,
- T. Roderick Docking,
- Isaac Y. Ho,
- Daniel S. Rokhsar,
- Rayan Chikhi,
- Dominique Lavenier,
- Guillaume Chapuis,
- Delphine Naquin,
- Nicolas Maillet,
- Michael C. Schatz,
- David R. Kelley,
- Adam M. Phillippy,
- Sergey Koren,
- Shiaw-Pyng Yang,
- Wei Wu,
- Wen-Chi Chou,
- Anuj Srivastava,
- Timothy I. Shaw,
- J. Graham Ruby,
- Peter Skewes-Cox,
- Miguel Betegon,
- Michelle T. Dimon,
- Victor Solovyev,
- Igor Seledtsov,
- Petr Kosarev,
- Denis Vorobyev,
- Ricardo Ramirez-Gonzalez,
- Richard Leggett,
- Dan MacLean,
- Fangfang Xia,
- Ruibang Luo,
- Zhenyu Li,
- Yinlong Xie,
- Binghang Liu,
- Sante Gnerre,
- Iain MacCallum,
- Dariusz Przybylski,
- Filipe J. Ribeiro,
- Shuangye Yin,
- Ted Sharpe,
- Giles Hall,
- Paul J. Kersey,
- Richard Durbin,
- Shaun D. Jackman,
- Jarrod A. Chapman,
- Xiaoqiu Huang,
- Joseph L. DeRisi,
- Mario Caccamo,
- Yingrui Li,
- David B. Jaffe,
- Richard E. Green,
- David Haussler,
- Ian Korf,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
...Illumina HiSeq data set of an unknown, simulated diploid . A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble...
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Methods: A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
- Aaron E. Tenney,
- Jia Qian Wu,
- Laura Langton,
- Paul Klueh,
- Ralph Quatrano,
- and Michael R. Brent
Genome Res. February 2007 17: 212-218; Published in Advance January 8, 2007, doi:10.1101/gr.5661407
...sequencer traces using phred. I. Accuracy assessment . Genome Res. 8 : 175 – 185 . ↵ Garsin, D.A. , Urbach, J. , Huguet-Tapia, J.C. , Peters, J.E. , Ausubel, F.M. ( 2004 ) Construction of an Enterococcus faecalis Tn917-mediated-gene-disruption library offers insight into Tn917 insertion patterns . J...
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Method: Genome assembly quality: Assessment and improvement using the neutral indel model
- Stephen Meader,
- LaDeana W. Hillier,
- Devin Locke,
- Chris P. Ponting,
- and Gerton Lunter
Genome Res. May 2010 20: 675-684; Published in Advance March 19, 2010, doi:10.1101/gr.096966.109
...for closely related species. Using two- or three-way alignments, the approach estimates the amount of aligned sequence containing clusters of nucleotides that were wrongly inserted or deleted during sequencing or assembly. Thus, the method is well-suited to assessing fine-scale sequence quality within single...
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METHODS: Automated Finishing with Autofinish
- David Gordon,
- Cindy Desmarais,
- and Phil Green
Genome Res. April 1, 2001 11: 614-625; doi:10.1101/gr.171401
...is that shotgun sequencing is highly automated but finishing is not: Most finishing decisions, such as which directed reads to obtain and which specialized sequencing techniques to use, are made by people. If finishing rates are to increase to match shotgun sequencing rates, most finishing decisions also must...
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Methods: Assessment of SAGE in Transcript Identification
- Erin D. Pleasance,
- Marco A. Marra,
- and Steven J.M. Jones
Genome Res. June 2003 13: 1203-1215; Published in Advance May 12, 2003, doi:10.1101/gr.873003
....C., and Green, P. 1998 . Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8 : 175 –185. ↵ FlyBase Consortium. 2002 . The FlyBase database of the Drosophila projects and community literature. Nucleic...
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METHODS: A Method For Parallel, Automated, Thermal Cycling of Submicroliter Samples
- Jonathan Nakane,
- David Broemeling,
- Roger Donaldson,
- Andre Marziali,
- Thomas D. Willis,
- Matthew O'Keefe,
- and Ronald W. Davis
Genome Res. March 1, 2001 11: 441-447; Published in Advance February 8, 2001, doi:10.1101/gr.164401
...traces using phred. I. Accuracy assessment. Genome Res. 8 : 175 – 185 . ↵ Meldrum D.R. ( 1997 ) A biomechatronic fluid-sample handling system for DNA processing. IEEE T. Mech. 2 : 99 – 109 . ↵ Meldrum D.R. , Evensen H.T. , Pence W.H. , Moody S.E. , Cunningham D.L. , Wiktor P.J. ( 2000 ) ACAPELLA-1K...
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METHODS: Mouse BAC Ends Quality Assessment and Sequence Analyses
- Shaying Zhao,
- Sofiya Shatsman,
- Bola Ayodeji,
- Keita Geer,
- Getahun Tsegaye,
- Margaret Krol,
- Elizabeth Gebregeorgis,
- Alla Shvartsbeyn,
- Daniel Russell,
- Larry Overton,
- Lingxia Jiang,
- George Dimitrov,
- Kevin Tran,
- Jyoti Shetty,
- Joel A. Malek,
- Tamara Feldblyum,
- William C. Nierman,
- and Claire M. Fraser
Genome Res. October 1, 2001 11: 1736-1745; Published in Advance September 20, 2001, doi:10.1101/gr.179201
...://www.tigr.org/tdb/bac_ends/mouse/bac_end_intro.html ), and ABI3700 capillary sequencers were used. Base calls were performed with phred ( Ewing and Green 1998 ; Ewing et al. 1998 ) and the quality scores were further adjusted with Paracel TraceTuner . Sequencing trimming was conducted with the program lucy ( http://www.tigr.org/softlab/ ) with criteria of (1...
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GENOME METHODS: Automated Sequence Preprocessing in a Large-Scale Sequencing Environment
- Michael C. Wendl,
- Simon Dear,
- Dave Hodgson,
- and LaDeana Hillier
Genome Res. September 1, 1998 8: 975-984; doi:10.1101/gr.8.9.975
.... Error probabilities. Genome Res. 8 : 186 – 194 . ↵ Ewing B.G. , Hillier L. , Wendl M.C. , Green P. ( 1998 ) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8 : 175 – 185 . ↵ Gleeson T. , Hillier L. ( 1991 ) A trace display and editing program for data from...

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