Searching journal content for articles similar to Simpson et al. 19 (6): 1117.

Displaying results 1-10 of 31

For checked items

view abstracts
download to citation manager

Select this article
RECOMB 2022 Special/Methods: Assembler artifacts include misassembly because of unsafe unitigs and underassembly because of bidirected graphs
- Amatur Rahman and
- Paul Medvedev
Genome Res. September 2022 32: 1746-1753; Published in Advance July 27, 2022, doi:10.1101/gr.276601.122
.... The theory and practice of sequence assembly. Annu Rev Genomics Hum Genet 16: 153–172. doi:10.1146/annurev-genom-090314-050032 ↵Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117–1123. doi:10.1101/gr.089532...
Select this article
Method: ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
- Shaun D. Jackman,
- Benjamin P. Vandervalk,
- Hamid Mohamadi,
- Justin Chu,
- Sarah Yeo,
- S. Austin Hammond,
- Golnaz Jahesh,
- Hamza Khan,
- Lauren Coombe,
- Rene L. Warren,
- and Inanc Birol
Genome Res. May 2017 27: 768-777; Published in Advance February 23, 2017, doi:10.1101/gr.214346.116
...to sequence s in the thousands and even millions, the development of efficient, scalable and accurate bioinformatics tools for producing high-quality reference draft s is timely. With ABySS 1.0, we originally showed that assembling the human using short 50-bp sequencing reads was possible by aggregating...
OPEN ACCESS ARTICLE
Select this article
Resource: De novo assembly of human genomes with massively parallel short read sequencing
- Ruiqiang Li,
- Hongmei Zhu,
- Jue Ruan,
- Wubin Qian,
- Xiaodong Fang,
- Zhongbin Shi,
- Yingrui Li,
- Shengting Li,
- Gao Shan,
- Karsten Kristiansen,
- Songgang Li,
- Huanming Yang,
- Jian Wang,
- and Jun Wang
Genome Res. February 2010 20: 265-272; Published in Advance December 17, 2009, doi:10.1101/gr.097261.109
...to DNA fragment assembly. Proc Natl Acad Sci 98: 9748–9753. Shendure J, Mitra RD, Varma C, Church GM. 2004. Advanced sequencing technologies: Methods and goals. Nat Rev Genet 5: 335–344. Simpson JT,Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: A parallel assembler for short read sequence...
Select this article
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
...- data sets into memory (ABySS) (Simpson et al. 2009), Chapman et al. (2011) (SOAPdenovo) (Li et al. 2010a), Cortex (in prep.). Now, as improvements in sequencer technology are extending the length of ‘‘short reads,’’ the overlap graph approach is being revisited, albeit with optimized programming...
OPEN ACCESS ARTICLE
Select this article
Resource: ECHO: A reference-free short-read error correction algorithm
- Wei-Chun Kao,
- Andrew H. Chan,
- and Yun S. Song
Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110
...and regarded every mismatch as a sequencing error. D2 (D. mel.) Another real data set we used is that of D. melanogaster inbred line RAL-399, sequenced and assembled by the Drosophila Population Genomics Project (DPGP, http://www. dpgp.org/). The short-reads were downloaded from the NCBI Sequence Read Archive...
Select this article
Resource: Dindel: Accurate indel calls from short-read data
- Cornelis A. Albers,
- Gerton Lunter,
- Daniel G. MacArthur,
- Gilean McVean,
- Willem H. Ouwehand,
- and Richard Durbin
Genome Res. June 2011 21: 961-973; Published in Advance October 27, 2010, doi:10.1101/gr.112326.110
...such variations. The first paradigm is to perform de novo assembly of short reads and detect indels by comparing contigs to a reference sequence. The second paradigm is to map each fragment directly and independently of other fragments to the reference sequence using a read mapper (e.g., Li et al. 2008; Langmead...
OPEN ACCESS ARTICLE
Select this article
Resource: Detecting copy number variation with mated short reads
- Paul Medvedev,
- Marc Fiume,
- Misko Dzamba,
- Tim Smith,
- and Michael Brudno
Genome Res. November 2010 20: 1613-1622; Published in Advance August 30, 2010, doi:10.1101/gr.106344.110
...Detecting copy number variation with mated short reads Paul Medvedev 1 , Marc Fiume 1 , Misko Dzamba 1 , Tim Smith 1 and Michael Brudno 1 , 2 , 3 1 Department of Computer Science, University of Toronto, Toronto, Ontario M5R...
Select this article
Methods: A new strategy for genome assembly using short sequence reads and reduced representation libraries
- Andrew L. Young,
- Hatice Ozel Abaan,
- Daniel Zerbino,
- James C. Mullikin,
- Ewan Birney,
- and Elliott H. Margulies
Genome Res. February 2010 20: 249-256; doi:10.1101/gr.097956.109
...SJ, Birol I. 2009. ABySS: A parallel assembler for short read sequence data. Genome Res 19: 1117– 1123. Sommer DD, Delcher AL, Salzberg SL, Pop M. 2007. Minimus: A fast, lightweight assembler. BMC Bioinformatics 8: 64. doi: 10.1186/ 1471-2105-8-64. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L...
Select this article
Method: TransMeta simultaneously assembles multisample RNA-seq reads
- Ting Yu,
- Xiaoyu Zhao,
- and Guojun Li
Genome Res. July 2022 32: 1398-1407; Published in Advance July 20, 2022, doi:10.1101/gr.276434.121
...Packer (Liu et al. 2016a), Bridger (Chang et al. 2015), Trinity (MacManes and Eisen 2013), ABySS (Simpson et al. 2009), SOAPdenovo-Trans (Xie et al. 2014), and IDBA-tran (Peng et al. 2013) have been available for reconstruction of full-length transcripts directly from RNA-seq reads. Generally speaking...
OPEN ACCESS ARTICLE
Select this article
Method: RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes
- Ka Ming Nip,
- Readman Chiu,
- Chen Yang,
- Justin Chu,
- Hamid Mohamadi,
- René L. Warren,
- and Inanc Birol
Genome Res. August 2020 30: 1191-1200; Published in Advance August 17, 2020, doi:10.1101/gr.260174.119
.... 2017. ABySS 2.0: resource-efficient assembly of large s using a Bloom filter. Genome Res 27: 768–777. doi:10.1101/gr.214346.116 ↵Jay TR, von Saucken VE, Landreth GE. 2017. TREM2 in neurodegenerative diseases. Mol Neurodegener 12: 56. doi:10.1186/s13024-017-0197-5 ↵Kim D, Paggi JM, Park C, Bennett C...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Simpson et al. 19 (6): 1117.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: