ライフサイエンスコーパス: sequencing read

1 weight algorithms for efficiently processing sequencing reads.

2 volume data, such as aligned next-generation sequencing reads.

3 s Mendelian transmission information and raw sequencing reads.

4 e only exome genotypes and ignore off-target sequencing reads.

5 rearrangements are readily detected from DNA sequencing reads.

6 Model or assemble haplotypes by overlapping sequencing reads.

7 LTR_retriever is also compatible with long sequencing reads.

8 is a challenge with short- and medium-length sequencing reads.

9 phisms into viral haplotypes from very short sequencing reads.

10 genes-information that is orthogonal to the sequencing reads.

11 ools that generate synthetic next-generation sequencing reads.

12 ng next-generation, short-insert, paired-end sequencing reads.

13 ents retains long-range information in short sequencing reads.

14 samples may contain 20-80% of mitochondrial sequencing reads.

15 involve hundreds of samples and billions of sequencing reads.

16 ylation status of adjacent CpG sites on long sequencing reads.

17 tions multiple kilobases apart directly from sequencing reads.

18 can be ascertained merely by generating more sequencing reads.

19 n essential step in most analysis done using sequencing reads.

20 e because of the sparseness and shortness of sequencing reads.

21 ed analysis toolkit for processing bisulfite sequencing reads.

22 tained by de novo assembly of 35,757,567 raw sequencing reads.

23 A sequencing and <20 h for processing of raw sequencing reads.

24 l assembly method that scales to millions of sequencing reads.

25 tification of genomic alterations from short sequencing reads.

26 nt allele fractions from possibly duplicated sequencing reads.

27 cultivar Khalas) and acquired 15,778,993 raw sequencing reads-about one million sequencing reads per

28 PoreSeq increases nanopore sequencing read accuracy of M13 bacteriophage DNA from 8

29 nome bisulphite sequencing, as 70-80% of the sequencing reads across these data sets provided little

30 Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such

31 The method was highly specific; 90% of sequencing reads aligned to targeted loci.

32 Analysis of sequencing reads allows contamination detection after se

33 ing individual investigators with integrated sequencing reads analysis, curation, and manipulation ca

34 echnologies, such as the short length of the sequencing reads and absence of mate-pair information.

35 Burrows-Wheeler Transform (BWT) index of the sequencing reads and an indexed database of microbial re

36 contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequ

37 data by mapping antigen receptor segments to sequencing reads and assembling the clonotypes, most of

38 teps necessary to process a large set of raw sequencing reads and create lists of gene transcripts, e

39 s (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies.

40 Based on ~30 million sequencing reads and more than 16,000 single-nucleotide

41 The protocol begins with raw sequencing reads and produces a transcriptome assembly,

42 The package accepts raw sequencing reads and provides the user with the genotypi

43 dual cells with a relatively small number of sequencing reads and that sequencing large numbers of si

44 tion process into two steps: the assembly of sequencing reads and the alignment of the resulting cont

45 both the incomplete information provided by sequencing reads and the nature of the genome itself.

46 ces was extended to apply to high-throughput sequencing reads and the strategies to estimate the corr

47 detected by evaluating a library of 402,554 sequencing reads and was later confirmed by Sanger seque

48 to report the potential loci of origin of a sequencing read, and not the base-to-base alignment by w

49 to sequence bias: GC content, mappability of sequencing reads, and regional biases that might be gene

50 the same regions with low numbers of aligned sequencing reads are also highly variable by genomic mic

51 een as peaks in enrichment profiles when the sequencing reads are mapped to a reference genome.

52 Note that alignment and analysis of RRBS sequencing reads are not covered in this protocol.

53 , and experiments requiring many millions of sequencing reads are now routine.

54 An advantage of scNOMe-seq is that sequencing reads are sampled independently of the access

55 f 100 kb, the scanning of 192 subclones with sequencing reads as short as 350 bp results in an approx

56 latform and obtained errors in our processed sequencing reads at a rate as low as 7.6 x 10(-6) per ba

57 nd random sampling of nucleotide types among sequencing reads at heterozygous sites present challenge

58 analyzing WGS and WES data is mapping short sequencing reads back to the reference genome.

59 rror correction Solution for high-throughput Sequencing reads (BLESS), uses a single minimum-sized Bl

60 ART generates simulated sequencing reads by emulating the sequencing process wit

61 anopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when

62 tation is complicated by the fact that short sequencing reads can match multiple organisms and by the

63 a DNA sequence from a collection of shotgun sequencing reads collected from it.

64 ions according to the observed counts of DNA sequencing reads containing the variant allele.

65 A total of 120,855 sequencing reads could be assigned to a germline Vkappa

66 Moreover, specific implementations for DNA sequencing read count data (based on a Negative Binomial

67 and universal method for processing per-base sequencing read count data called FIXSEQ.

68 Also, the properties of sequencing read counts can be leveraged to achieve a mor

69 , resulting in a non-uniform distribution of sequencing read counts for each base position in a gene.

70 persion rate on the base-level proportion of sequencing read counts from two samples.

71 allele fraction of this fusion, based on RNA-sequencing read counts.

72 These labels allow one to combine multiple sequencing reads covering the same RNA molecule to reduc

73 CA, USA) provides the longest continuous DNA sequencing reads currently available.

74 emerged as a common file format for sharing sequencing read data combining both the sequence and an

75 erformance of HapTree on simulated polyploid sequencing read data modeled after Illumina sequencing t

76 in-species DNA sample contamination based on sequencing read data, showed that our methods can reliab

77 method (STITCH) for imputation based only on sequencing read data, without requiring additional refer

78 ions and assign parental haplotypes with low sequencing read depth and of unknown phase.

79 hmarked against copy numbers determined from sequencing read depth to successfully obtain CNP genotyp

80 copy number variants (CNVs) from human exome sequencing read depth, but previous tools have not been

81 in most of the extraneous variability in the sequencing read depth: GC content, target footprint size

82 Conversely, approximately 10% of the sequencing reads derived from each isolate fail to align

83 cally, we analyzed over 500 million Illumina sequencing reads derived from the hippocampi of 10 colon

84 Sequencing reads derived from three libraries, obtained

85 e quantification relies entirely on counting sequencing reads, detailed studies about the method's ac

86 tional modules directly from high-throughput sequencing reads, enabling the determination of communit

87 cluding genome assembly, error correction of sequencing reads, fast multiple sequence alignment and r

88 ulator Wessim that generates synthetic exome sequencing reads from a given sample genome.

89 However, sequencing reads from bisulfite-converted DNA can vary s

90 apping should facilitate de novo assembly of sequencing reads from complex regions in diploid organis

91 stical tests to evaluate the distribution of sequencing reads from different plates into contigs, and

92 The alignment of sequencing reads from fusion transcript loci in cancer g

93 We present an approach that uses sequencing reads from high-throughput sequencing of bisu

94 RINS accurately identifies sequencing reads from intact or mutated non-human genome

95 Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compar

96 By aligning the sequencing reads from multiple genotypes we detected 23,

97 ant Assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and sin

98 nd applied this model to 325 920 unique deep sequencing reads from plasma virus samples from 45 drug

99 Using simulated sequencing reads from real individual genotypes in the H

100 Long sequencing reads from targeted regions maintain the stru

101 omposition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer.

102 We therefore generated 130x coverage by long sequencing reads from the Pacific Biosciences platform t

103 Long sequencing reads generated by single-molecule sequencing

104 assessed the performance of the method using sequencing reads generated from reference DNA with known

105 With a broad scope spanning raw sequencing reads, genome assemblies and functional annot

106 About 1,344.04 million sequencing reads have been generated from sixteen librar

107 SplicePlot takes mapped RNA sequencing reads in BAM format and genotype data in VCF

108 SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data i

109 encing (HTS) data are commonly stored as raw sequencing reads in FASTQ format or as reads mapped to a

110 , we estimated GSTM1 copy number using exome sequencing reads in the Atherosclerosis Risk in Communit

111 totals 1.68% of all human faecal metagenomic sequencing reads in the public databases.

112 for phasing variants that are overlapped by sequencing reads, including those from RNA sequencing (R

113 Network analysis of de novo assembled sequencing reads into 52,556 scaffolds identified ARGs l

114 convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset

115 Our use of informative sequencing reads is formulated as a discrete dynamic Bay

116 , machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as

117 microbial community from unannotated shotgun sequencing reads is one of the important goals in metage

118 l and robust method to detect CNV from short sequencing reads is proposed in this study.

119 Quantitative measures of sequencing read length (Phred Q30 count) and real-time P

120 bacteria, these advances come at the cost of sequencing read length, limiting the phylogenetic resolu

121 arryover contamination or degradation in the sequencing read length.

122 ion time but also produced a decrease in the sequencing read length.

123 R genotyping, depending on repeat length and sequencing read length.

124 Approximately 70% of the unique sequencing reads map to previously annotated protein-cod

125 in technical details of library preparation, sequencing, read mapping, normalization, gene sets, and

126 lation BWT and use it to store and index the sequencing reads of 2705 samples from the 1000 Genomes P

127 es the physical distances between paired-end sequencing reads of a library of a wild-type reference F

128 d Salmonella serotype determination from raw sequencing reads of fecal metagenomes from mice orally i

129 Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in lengt

130 This allows multiple sequencing reads of the same product to be compared so t

131 17,676 viral contigs assembled from shotgun sequencing reads of VLP DNAs, we identified viruses that

132 and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content.

133 e MinION nanopore sequencer can produce long sequencing reads on a device similar in size to a USB me

134 millions of chimpanzee whole-genome shotgun sequencing reads onto the human genome.

135 arising as a result of identifying genes on sequencing reads or on assembled nucleotide contigs, whi

136 rich regions, where short primers yield poor sequencing reads or PCR yields.

137 provides a flexible framework for extracting sequencing reads or read-pairs that satisfy combinations

138 ted shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-seq

139 ncertainty as to which epiallele an observed sequencing read originated from is explicitly incorporat

140 rocessed to sequencing libraries wherein all sequencing reads originating from each long DNA molecule

141 ncluding de novo assembly of high throughput sequencing reads, ortholog identification, multiple sequ

142 Starting with next-generation sequencing reads, PALEOMIX carries out adapter removal,

143 8,993 raw sequencing reads-about one million sequencing reads per library-and the pooled sequences we

144 weekly production is approximately 100, 000 sequencing reads per week.

145 tively examine the statistical properties of sequencing reads produced by Illumina Genome Analyzer an

146 transcript assembly problem) from the short sequencing reads produced by RNA-seq protocol plays a ce

147 Allele-specific sequencing reads provide a powerful signal for identifyi

148 From the raw sequencing reads, Purc was able to accurately infer the

149 data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate geno

150 ind a characteristic region of enrichment in sequencing reads relative to gene annotations.

151 As a result, error correction of sequencing reads remains an important problem.

152 embling a large genome using next generation sequencing reads requires large computer memory and a lo

153 s show differing amounts of FFPE damaged DNA sequencing reads revealed as relatively high alignment m

154 For sequencing read-sized queries of 500 bp, an order of mag

155 We present G-SQZ, a Huffman coding-based sequencing-reads-specific representation scheme that com

156 stics to identify peak-like distributions of sequencing reads, taking advantage of improved peak defi

157 psy specimens revealed more than 2.5 million sequencing reads that did not match known organisms.

158 Considering only sequencing reads that map uniquely onto the human genome

159 of their results due to the small number of sequencing reads that were confidently assigned to wheat

160 imited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasin

161 Longer sequencing reads tip the ratio strongly toward increased

162 package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation re

163 al RNA-seq data analysis, including aligning sequencing reads to a genome, constructing transcriptome

164 Methods that utilize these technologies map sequencing reads to a reference genome and look for sign

165 Many programs for aligning short sequencing reads to a reference genome have been develop

166 Seq requires the mapping of relatively short sequencing reads to a reference genome or transcript set

167 need much faster software to map these long sequencing reads to a reference genome to identify SNPs

168 echnical artifacts such as errors in mapping sequencing reads to a reference genome, sequencing error

169 ze in the alignment of short next-generation sequencing reads to a reference sequence.

170 VNTRseek maps sequencing reads to a set of reference TRs and then iden

171 ementing quasi-mapping-is capable of mapping sequencing reads to a target transcriptome substantially

172 The alignment of sequencing reads to a transcriptome is a common and impo

173 rithm implementing this approach for mapping sequencing reads to a transcriptome.

174 ng different types of ChIA-PET data from raw sequencing reads to chromatin loops.

175 at iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome s

176 ties involved in properly apportioning short sequencing reads to highly repetitive regions of the gen

177 the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy.

178 hemical probing methods generate millions of sequencing reads to provide structural constraints for R

179 hich uses the fluctuation spectrum of mapped sequencing reads to quantify and compare chromatin patte

180 Fragment recruitment, a process of aligning sequencing reads to reference genomes, is a crucial step

181 ed a bioinformatics pipeline that attributes sequencing reads to specific KIR genes, determines copy

182 indicate that NBC can assign next-generation sequencing reads to their taxonomic classification and c

183 g from 44.8-96.5%, and representation of CPV sequencing reads to those of the metagenome background r

184 g the multiple steps required to go from raw sequencing reads to variant discovery.

185 n tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyse

186 We used the original sequencing reads (trace archives) available through the

187 We present svviz, a sequencing read visualizer for SVs that sorts and displa

188 Through clustering of sequencing reads we can determine both number of OTUs an

189 Ninety six percent of the sequencing reads were assembled into scaffolds of >500 b

190 Whole-genome sequencing reads were from a lymphoblastoid cell-line.

191 Ninety percent of all sequencing reads were from targeted exons, demonstrating

192 Capture sequencing reads were generated from primary lymphoid tu

193 When these sequencing reads were mapped onto the assembled Unigenes

194 Sequencing reads were mapped using GSMAPPER, BFAST, and

195 lular burden, viable monocyte count, and RNA sequencing reads were performed up to 28 days.

196 Sequencing reads were processed and aligned to the refer

197 cut site-adjacent sequence fragments had no sequencing reads whereas a portion had substantially gre

198 This generates millions of sequencing reads, which are then analyzed using a fully

199 pping algorithm designed to analyse nanopore sequencing reads, which progressively refines candidate

200 with shorter but much more accurate Illumina sequencing reads, whose error rates average <1%.

201 l pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative

202 anopore MinION are capable of producing long sequencing reads with average fragment lengths of over 1

203 EST), an algorithm that uses next-generation sequencing reads with partial alignments to a reference

204 plotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length,

205 phylogenetics directly from next-generation sequencing reads without the use of a reference genome.