[PDF] Top 20 Error Correction and de novo Genome Assembly of DNA Sequencing Data
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Error Correction and de novo Genome Assembly of DNA Sequencing Data
... the assembly process in SAGE was very aggressive, which re- sulted in longer contigs and sca ff olds, but also caused many ...assemble data sets that have reads with the same ...multiple data sets, ... See full document
143
Error Correction in Next Generation DNA Sequencing Data
... Accurate Correction of Errors in Reads), an error correction program that targets the Illumina genome sequencer, which is currently the dominant NGS ...advanced data structures with an ... See full document
44
Correction of DNA Sequencing Data with Spaced Seeds
... greedy error correction algorithm that looks for the region of longest trusted k-mers that appear in Bloom filter B, and attempts to stretch this region by introducing substitution to the adjacent ... See full document
62
Optimized Illumina PCR free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly
... sequence assembly as long as read length (or the insert size of a read pair) is not capable of spanning the ...hybrid error correction or self-correction approaches to enhance PacBio’s ... See full document
14
Detecting Staphylococcus aureus Virulence and Resistance Genes: a Comparison of Whole Genome Sequencing and DNA Microarray Technology
... of error re- mained ...the de novo assembled ...of error: (i) failures of de novo assembly (target was identified in reference-mapped ge- nome), (ii) insufficient ... See full document
9
Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications
... reference genome, theoretically predicted protein sequences, and transcriptome sequencing (RNA-Seq)-derived tran- script sequences gave rise to so-called proteogenomics approaches (1, ...the ... See full document
17
Resequencing and assembly of seven complex loci to improve the Leishmania major (Friedlin strain) reference genome
... genomic DNA the region containing the putative missed gene ...After sequencing, we noticed that not only the contigs Cg12150 and Cg12136 were contained in this region, but two other de novo ... See full document
13
Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape
... First, transcripts present in the individual datasets but omitted by Cuffmerge were re-integrated. In some in- stances, reference transcripts were wrongly assigned FPKM values of 0 by Cufflinks, and re-quantifying the ... See full document
17
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism
... and sequencing were performed at GATC Biotech AG (Konstanz, ...for assembly. Pacific Biosciences sequencing data were assembled using an implemented version of PacBio SMRT Analysis, version ... See full document
9
Methods for De-novo Genome Assembly
... the assembly process is a set of reads that are passed through all data preprocessing ...graph data structure in the heart of each assembly pipeline called the assembly ...small ... See full document
20
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
... The de Bruijn graph of a set of DNA or RNA sequences is a data structure which plays an increasingly impor- tant role in next-generation sequencing ...perform de novo ... See full document
9
Assessment of Genome-Wide Genetic and Epigenetic De Novo Variation in Families with Monozygotic Twins Discordant for Schizophrenia
... Generation Sequencing (NGS) coverage (Baranzini et ...where DNA sequence differences exist between identical twins, genotypes usually show unexpected ratios, that is, instead of identifying expected ... See full document
331
De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
... in genome organization compared to the reference strain ...CEN.PK113-7D genome relative to ...CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes ... See full document
17
Comparative studies of Toxoplasma gondii transcriptomes: insights into stage conversion based on gene expression profiling and alternative splicing
... by de novo as- sembly [18] (Additional file 7: file ...this sequencing error, we confirmed some of the UTR regions by assem- bled fragments that hit both of the ... See full document
11
De novo construction of a “Gene space” for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources
... is de facto very difficult if not impossible because these sequences have multiple locations in the ...sequence data, is an effective and economical ... See full document
9
Characterization of the Ren4 resistance locus through the integration of de novo assembly, expression analysis, and Genotyping-by-Sequencing data
... transcript graphs. Initially, Chrysalis recursively clusters linear contigs provided by inchworm to define component clusters which contain contigs thought to be derived from the same gene as a result of alternative ... See full document
64
MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies
... steps de- scribed above, this is regulated by the use of the option ‘--from-stage’ with one of the four keywords (consensus, coords, orfs or flanks) corresponding to the analysis steps from 2nd to ...other ... See full document
8
Genome sequence of Coxiella burnetii strain Namibia
... Because of the highly infectious nature of C. burnetii, cultivation should not be attempted outside adequate BSL 3 laboratories. Even with these, isolation is a difficult and very time-consuming procedure. Moreover, ... See full document
9
Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1
... the 4509 predicted genes, 4438 (98.42 %) were protein- coding, and 3505 (77.73 %) annotated with putative func- tion. Pseudogenes were not detected. Genes not linked to a function were annotated as hypothetical or ... See full document
11
Evolution in a marine gastropod : rocks, clocks, DNA and diversity : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Evolutionary Biology
... The incongruence of population-level mutation rates and species-level substitution rates is a known issue (Ho and Larson 2006) that requires further analysis. Such a study should be carried out in a group of species for ... See full document
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