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Resource: SNP detection for massively parallel whole-genome resequencing
- Ruiqiang Li,
- Yingrui Li,
- Xiaodong Fang,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- and Jun Wang
Genome Res. June 2009 19: 1124-1132; Published in Advance May 6, 2009, doi:10.1101/gr.088013.108
...resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed this method by carefully considering the data quality, alignment, and experimental errors common to this technology. All of this information...
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Methods: A probabilistic approach for SNP discovery in high-throughput human resequencing data
- Rose Hoberman,
- Joana Dias,
- Bing Ge,
- Eef Harmsen,
- Michael Mayhew,
- Dominique J. Verlaan,
- Tony Kwan,
- Ken Dewar,
- Mathieu Blanchette,
- and Tomi Pastinen
Genome Res. September 2009 19: 1542-1552; Published in Advance July 15, 2009, doi:10.1101/gr.092072.109
...and FCR, as the majority of hets are assigned score 0. Probabilistic SNP discovery in resequencing data Genome Research 1545 www..org actually correct. Out of the 52 high-confidence heterozygous calls conflicting with HapMap that were tested, 51 (98%) were actually heterozygous, while seven of 10 tested...
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Resource: A SNP discovery method to assess variant allele probability from next-generation resequencing data
- Yufeng Shen,
- Zhengzheng Wan,
- Cristian Coarfa,
- Rafal Drabek,
- Lei Chen,
- Elizabeth A. Ostrowski,
- Yue Liu,
- George M. Weinstock,
- David A. Wheeler,
- Richard A. Gibbs,
- and Fuli Yu
Genome Res. February 2010 20: 273-280; Published in Advance December 17, 2009, doi:10.1101/gr.096388.109
...to different sequencing-by-synthesis chemistries as well as different base-calling algorithms. The quality scores from current platform algorithms are often not accurate enough to differentiate true SNPs from sequencing errors. Nevertheless, significant biases in the error rates—as a function of the qualities...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...nucleotide polymorphism (SNP) diversity between the populations. We find that ancient housekeeping genes are a major source of the overall isoform diversity, and that the generation of alternative first exons plays a major role in generating new isoforms. Given that our data allow us to distinguish between...
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Letter: High-resolution analysis of epigenetic changes associated with X inactivation
- Hendrik Marks,
- Jennifer C. Chow,
- Sergei Denissov,
- Kees-Jan Françoijs,
- Neil Brockdorff,
- Edith Heard,
- and Hendrik G. Stunnenberg
Genome Res. August 2009 19: 1361-1373; Published in Advance July 6, 2009, doi:10.1101/gr.092643.109
...show a female-specific quantitative increase of H3K27me3 across the X chromosome as XCI proceeds in differentiating female ES cells. Using female ES cells with nonrandom XCI and polymorphic X chromosomes, we demonstrate that this increase is specific to the Xi by allele-specific SNP mapping of the Ch...
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Resource: BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing
- Wei-Chun Kao,
- Kristian Stevens,
- and Yun S. Song
Genome Res. October 2009 19: 1884-1895; Published in Advance August 6, 2009, doi:10.1101/gr.095299.109
...sub-strings from low-quality reads has been shown to improve coverage under a global alignment model (Rougemont et al. 2008). Recently, Brockman et al. (2008) have suggested a general method to define more accurate quality scores in sequencing-by-synthesis systems and applied it to data from the 454...
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Resource: Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
- Wei Qu,
- Shin-ichi Hashimoto,
- and Shinichi Morishita
Genome Res. July 2009 19: 1309-1315; Published in Advance May 13, 2009, doi:10.1101/gr.089151.108
...WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. 2008. Quality scores and SNP detection in sequencing-by-synthesis systems.Genome Res 18: 763–770. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: De novo assembly of whole shotgun microreads. Genome Res...
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REVIEW: Pyrosequencing Sheds Light on DNA Sequencing
- Mostafa Ronaghi
Genome Res. January 1, 2001 11: 3-11; doi:10.1101/gr.150601
...makes typing extremely accurate and easy. Relative standard deviation values for the ratio between key peaks of the respective SNPs and reference counterparts are ⋜0.1 ( Alderborn et al. 2000 ). Simple manual comparison of predicted SNP patterns and the raw data obtained from the PSQ 96 system can score...
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Perspective: Challenges and considerations for reproducibility of STARR-seq assays
- Maitreya Das,
- Ayaan Hossain,
- Deepro Banerjee,
- Craig Alan Praul,
- and Santhosh Girirajan
Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
...be sourced from commercially available DNA repositories (Liu et al. 2017b), specific populations carrying noncoding mutations or SNPs to be assayed (Liu et al. 2017a), cultured bacterial artificial chromosomes (BACs) (Arnold et al. 2013), or custom oligo pools (Kalita et al. 2018). Different sources have...
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Methods: High-throughput genotyping by whole-genome resequencing
- Xuehui Huang,
- Qi Feng,
- Qian Qian,
- Qiang Zhao,
- Lu Wang,
- Ahong Wang,
- Jianping Guan,
- Danlin Fan,
- Qijun Weng,
- Tao Huang,
- Guojun Dong,
- Tao Sang,
- and Bin Han
Genome Res. June 2009 19: 1068-1076; Published in Advance May 6, 2009, doi:10.1101/gr.089516.108
...was assigned at this nucleotide position. From high-quality sequences obtained for the 150 RILs, a total of 1,493,461 SNPs were detected, which gave an average density of 25 SNPs/Mb or 1 SNP every 40 kb for the RILs. Genotype calling When SNPs detected from the RILs were placed along the chromosomes, we found...
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