Fast and accurate mapping of next generation sequencing data

... due to sequencing errors For NGS sequencers like Illumina and SOLiD, the majority of sequencing errors are of this type The ﬁrst contribution of this thesis is the introduction of a fast and memory-eﬃcient ... overview of the importance and applications of genomic sequencing We will now present a review of the technologies behind genome sequencing 2.4.1 Sanger Sequencing Sanger sequencing uses the idea of ... from an algorithmic point of view, processing the output of sequencing machines pose two distinct challenges; the volume of the data and sequencing errors The volume of the data will keep on increasing...

báo cáo khoa học: " Overcoming bias and systematic errors in next generation sequencing data" ppt

... frequent in reads that align to the SNP site only at later sequencing cycles, indicating a technical bias in base calls at this position, while the plot in (b) shows a strong reduction in this bias In ... Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores Genome Res 2008, 18:1851-1858 doi:10.1186/gm208 Cite this article as: Taub MA, et al.: Overcoming bias ... Dudoit S: Biases in Illumina transcriptome sequencing caused by random hexamer priming Nucleic Acids Res 2010, 38:e131 24 Li J, Jiang H, Wong WH: Modeling non-uniformity in short-read rates in RNA-Seq...

Báo cáo y học: "Genomics through the lens of next-generation sequencing" potx

... ecologically differentiated by a set of niche-specific genes Finally, James Taylor (Emory University, Atlanta, USA) offered an integrated vision of how we might aim to science in the age of next-generation ... large-scale analyses that potentially involve multiple software programs, while maintaining Page of the transparent provenance of the data and parameters The resulting record of every step of the workflow ... are likely to be quite rare So, while rare variants may or may not explain the ‘missing heritability’ problem, they are not a probable cause of the associations already discovered by GWAS One...

Báo cáo y học: "Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA" pot

... Page 12 of 12 doi:10.1186/gb-2010-11-10-r99 Cite this article as: Homer and Nelson: Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA ... Local re-alignment of simulated data Local re-alignment of empirical data To assess the performance of local re-alignment on a dataset with a known diploid sequence, two whole genome human re -sequencing ... respectively, and after SRMA were 0.434, 0.538, and 0.328, respectively This demonstrates the ability of SRMA to improve variant calling, especially for indels To further examine the accuracy of the variant...

Báo cáo y học: "IA simple, fast, and accurate method of phylogenomic inference" docx

... performance of the phylogeny based and the similarity based phylotyping, we carried out a simulation study We determined the sensitivity and specificity of the taxonomic assignments made by AMPHORA and ... 0.1 0.1 0 phylum class order family genus species phylum class order family genus species Figure Comparison of the phylotyping performance by AMPHORA and MEGAN Comparison of the phylotyping performance ... the sensitivity and specificity of phylotyping methods were calculated as described in the report by Krause and coworkers [39] Briefly, for a taxon i, let Pi be the number of query sequences from...

Báo cáo y học: " Evaluation of next generation sequencing platforms for population targeted sequencing studies" pot

... platform may be more useful for identifying indels than the ABI Sanger technology The Illumina GA and ABI SOLiD platforms at the time of this analysis were unable to identify indels automatically ... is typically employed in targeted sequencing studies utilizing NGS technologies Conclusions Our results suggest that to effectively balance cost and data quality for population targeted sequencing ... accuracies reported here are likely to be more indicative of the real performance of NGS platforms for de novo detection of variants in human sequences Interestingly, our analysis indicates that ABI Sanger...

Paired end transcriptome assembly and genomic variants management for next generation sequencing data

... PETA and UASIS, to interpret and analyze large scale of Next Generation Sequencing data They serve as fundamental components to provide accurate transcriptomes and better data management for related ... PETA (Paired End Transcriptome Assembler) We claim that the full utilization of raw reads and paired- end information is able to construct a cleaner splicing graph and generate more accurate and ... 1.4 Next Generation Sequencing Maxam-Gilbert sequencing and Sanger sequencing (28) are called first generation sequencing technologies Although they are introduced at the same time, Sanger sequencing...

Báo cáo hóa học: " Fast and Accurate Ground Truth Generation for Skew-Tolerance Evaluation of Page Segmentation Algorithms" potx

... absolute performance of a system In other words, it means a comparison between the performance of our method of GT generation and that of the ideal one Though the IGT is also block-based, its generation ... accuracy of ground truth generation with GROTTO Finally, Figure provides the distributions over the whole angle range from −90◦ to +90◦ in 1◦ steps for cases 1, 4, and 10 For angles of 0, −90, and ... the occurrence of cases and That is, when the number of case is large for a particular angle, that of case is small for the same angle, and vice versa The average time for SGT generation, excluding...

Báo cáo y học: "Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcript" ppt

... caacctctgggttcagcttttgccaagcttcagGTGTTTGCACACCGTTAGAAATTACCACAAATGGTTGAAAAATC T S G F S F C Q A S G V C T P L E I T T N G STOP NUP214 (exon 29) XKR3 (exon 4) caacctctgggttcagcttttgccaagcttcagCATTGCTGATGACATTTTCCCTGTTATCAGTTACTTATGGGGC ... cDNA libraries PR and AM performed the hybrid selection MFB and JZL analyzed the sequence data XA and AG confirmed fusion transcripts and SNPs, respectively JZL, CN, LAG, and AG conceived and ... bias in sequence composition of fusion- transcript cDNA fragments NUP214 (exon 29) XKR3 (exon 2) caacctctgggttcagcttttgccaagcttcagCACCCTGAGAATGGAGACAGTGTTTGAAGAGATGGATG T S G F S F C Q A S A P...

Báo cáo y học: "Comparison of solution-based exome capture methods for next generation sequencing" doc

... between the capture methods Of all 2,596 indel positions identified with any one of the methods, 241 were identified by all four methods, 492 by any three methods and 1,130 by any two methods; 119 ... for Health and Welfare, Helsinki, Finland In addition, we estimated the performance of different exome capture methods by auditing the quality and quantity of exome sequencing data produced for ... by using pg of the captured sample and 14 cycles of PCR for the NimbleGen SeqCap and 10 pg of the captured sample and 16 cycles of PCR for the Agilent SureSelect Stratagene Herculase II enzyme...

Báo cáo y học: "High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing" ppsx

... Detection System; shALIGN: shRNA Alignment; shRNA: short hairpin RNA; shRNAmir: shRNA encoded within a miRNA; shRNAseq: shRNA Sequencing; sinLTR: self-inactivating LTR; TAMRA: tetramethylrhodamine; ... massively parallel sequencing - 31 - shRNA library glycerol stock shRNA library plasmid shRNA library virus Image analysis Target cell infection Base calling e ca Puromycin selection Library alignment ... computational pipeline to analyse NGS data from shRNA screens and describe two open source analysis packages, shALIGN and shRNAseq, designed to simplify barcode screen analysis Using shRNA pools with engineered...

ANALYSIS OF INTEGRATION SITES OF TRANSGENIC SHEEP GENERATED BY LENTIVIRAL VECTORS USING NEXT-GENERATION SEQUENCING TECHNOLOGY

... i ANALYSIS OF INTEGRATION SITES OF TRANSGENIC SHEEP GENERATED BY LENTIVIRAL VECTORS USING NEXT-GENERATION SEQUENCING TECHNOLOGY A Thesis Submitted to the Faculty of Purdue University by Yu-Hsiang ... August 2013 Analysis of Integration Sites of Transgenic Sheep Generated by Lentiviral Vectors Using Next-Generation Sequencing Technology Major Professor: Anna Malkova The development of new methods ... products of transgenic sheep fetal tissues-animal 709-2 22 Figure 4.4 LAM-PCR products of transgenic sheep fetal tissues-animal 498-1 23 Figure 4.5 LAM-PCR products of transgenic sheep fetal...

Investigating lipid and secondary metabolisms in plants by next generation sequencing

... Investigating lipid and secondary metabolisms in plants by next- generation sequencing JIN JINGJING (B.COMP., SCU) (B.ECOM., SCU) A THESIS SUBMITTED ... ligation and singlemolecule sequencing Sequencing by synthesis involves taking a single strand of the DNA to be sequenced and then synthesizing its complementary strand enzymatically The pyrosequencing ... and plant pollination Next- generation sequencing has been widely used for understanding plant metabolisms By using next- generation sequencing, draft genomes for unknown species and markers for...

Identification of genomic alterations in castration resistant prostate cancer using next generation sequencing

... binding domain, and the ligand binding domain (LBD) The “hinge domain” links the LBD to the DBD (42) (Figure 6) Figure 6: Schematic representation of AR on Chromosome X (43) Upon the binding of ... CTD-2310E8 RP11-188K5 Invitrogen Invitrogen Invitrogen Invitrogen Invitrogen Invitrogen Invitrogen Invitrogen Invitrogen 33 Methods 6.1 Next generation sequencing (SOLiD4) DNA Extraction ... using the SOLiD4 sequencing platform Objective III: Identification of novel therapeutic targets for castration resistant prostate cancer by whole exome sequencing, and functional validation of...

Tài liệu Báo cáo khoa học: "Fast and Robust Part-of-Speech Tagging Using Dynamic Model Selection" pptx

... 92.50 92.32 Table 3: Tagging accuracies of all tokens (in %) Models D and G indicate domain-speciﬁc and generalized models, respectively and Model S indicates the dynamic model selection approach ... The dynamic model selection approach (Model S) shows the most robust results across genres, although Models D and G still can perform Some semi-supervised and domain-adaptation approaches using ... POS tagging and model selection tokens / sec Stanford 421 SVMTool 1,163 Model S 31,914 Table 5: Tagging speeds Conclusion We present a dynamic model selection approach that improves the robustness...

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