ライフサイエンスコーパス: sequencing read

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

2 tions multiple kilobases apart directly from sequencing reads.

3 can be ascertained merely by generating more sequencing reads.

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

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

6 ed analysis toolkit for processing bisulfite sequencing reads.

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

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

9 tification of genomic alterations from short sequencing reads.

10 address the ambiguities caused by repetitive sequencing reads.

11 nt allele fractions from possibly duplicated sequencing reads.

12 weight algorithms for efficiently processing sequencing reads.

13 mputing CpG methylation states on individual sequencing reads.

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

15 s Mendelian transmission information and raw sequencing reads.

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

17 rearrangements are readily detected from DNA sequencing reads.

18 Model or assemble haplotypes by overlapping sequencing reads.

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

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

21 ools that generate synthetic next-generation sequencing reads.

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

23 izing multiple-type sensitivity with minimal sequencing reads.

24 oped to detect DNA methylation from nanopore sequencing reads.

25 ols demands simulators to generate realistic sequencing reads.

26 immune infiltrate and presence of bacterial sequencing reads.

27 an other tools utilizing shotgun metagenomic sequencing reads.

28 ask of identifying the origin species of DNA sequencing reads.

29 from C57BL/6 genomic DNA using only 200 000 sequencing reads.

30 expression due to the uneven distribution of sequencing reads.

31 th highly degraded DNA samples or ultrashort sequencing reads.

32 rence genomes with abnormal pileups of short sequencing reads.

33 ies are spurious artifacts of clustering 16S sequencing reads.

34 detect DNA methylation states from Nanopore sequencing reads.

35 collections of pre-phased variants and long sequencing reads.

36 nerated 710 datasets constituting 57 billion sequencing reads.

37 heterozygous polyploids from Illumina short-sequencing reads.

38 and plasmids was achieved using 100,000 raw sequencing reads.

39 cluding pathogens amid the plethora of human sequencing reads.

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

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

42 LTR_retriever is also compatible with long sequencing reads.

43 phisms into viral haplotypes from very short sequencing reads.

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

45 vel reference-free approach to analyze short sequencing reads.

46 involve hundreds of samples and billions of sequencing reads.

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

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

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

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

51 axonomic classification method that compares sequencing reads against a microbial genome database.

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

53 expression data can be extracted using only sequencing read alignments without cell sorting.

54 Analysis of sequencing reads allows contamination detection after se

55 Streaming the sequencing reads allows this approach to sustain mapping

56 Variant analysis of sequencing reads also allowed the identification of poli

57 From raw sequencing reads, amplimap generates output such as read

58 g DuploMap-aligned PacBio circular consensus sequencing reads, an additional 8.9 Mb of DNA sequence w

59 quantification from short-read transcriptome sequencing reads, an R library for data visualization, a

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

61 for secure, efficient and reliable access to sequencing read and variation data.

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

63 bonobo and orangutan Ys from short and long sequencing reads and aligned them with the publicly avai

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

65 assembled from hybrid Illumina and Nanopore sequencing reads and annotated.

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

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

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

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

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

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

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

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

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

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

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

77 uired to separate sequin- and sample-derived sequencing reads and to evaluate the diagnostic performa

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

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

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

81 om short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annot

82 algorithms use a haplotype reference panel, sequencing reads, and/or parental genotypes to phase an

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

84 ling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome c

85 Although long single molecule sequencing reads are better able to resolve genomic repe

86 PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly acc

87 For each single cell, DNA-sequencing reads are computationally arranged into spati

88 equencing (snATAC-seq) feature matrices from sequencing reads are inconsistent, affecting downstream

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

90 Hundreds of millions of sequencing reads are needed to get good coverage of CLas

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

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

93 Typically, raw sequencing reads are processed into a gene expression ma

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

95 The resulting sequencing reads are then mapped with the T>C-aware alig

96 Falsely classifying sequencing reads as originating from pathogens can lead

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

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

99 signed to select and store only high-quality sequencing reads at extremely high compression rates.

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

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

102 al sample was obtained by demultiplexing the sequencing reads based on the indexes.

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

104 ics by providing a scaffold for alignment of sequencing reads, but currently only reflects a single c

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

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

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

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

109 bled from single-molecule, real-time shotgun sequencing reads collinear with an optical map.

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

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

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

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

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

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

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

117 Beta-binomial modelling of sequencing read counts was used to infer KEAP1 clonal in

118 Beta-binomial modelling of sequencing read counts was used to infer mutation clonal

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

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

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

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

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

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

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

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

127 software tool that utilizes next-generation sequencing read depth information and variant allele fre

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

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

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

131 1218 1000 Genomes Project phase 3 males from sequencing read-depth, then chose 14 for valid ation by

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

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

134 Sequencing reads derived from three libraries, obtained

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

136 molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes

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

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

139 nchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content

140 ses the rate of mapping of rumen metagenomic sequencing reads from 15% to 50-70%.

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

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

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

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

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

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

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

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

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

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

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

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

153 Long sequencing reads from targeted regions maintain the stru

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

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

156 Long sequencing reads generated by single-molecule sequencing

157 to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample.

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

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

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

161 t quantify variability in DNA methylation in sequencing reads have been proposed.

162 resource of 563 million full-length isoform sequencing reads identifies 201 novel, potentially prote

163 whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of synten

164 matics pipeline was developed to process raw sequencing reads, identify antibiotic resistance genetic

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

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

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

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

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

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

171 141K mutant allele in 25% of next-generation sequencing reads indicating somatic mosaicism, whereas C

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

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

174 highly effective for classifying metagenomic sequencing reads into different groups.

175 puting the two haplotypes that partition the sequencing reads into two disjoint sub-sets, with the le

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

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

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

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

180 counts of substrings of length k from longer sequencing reads, k-mers, as genotyping data.

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

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

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

184 arryover contamination or degradation in the sequencing read length.

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

186 nd by the presence of SVs that vastly exceed sequencing read lengths.

187 veloped a toolkit, 'MetaSIPSim,' to simulate sequencing read libraries for metagenomic-SIP experiment

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

189 Conventional strategies either sum up all sequencing reads mapped to a parental RNA, which sacrifi

190 with and without enrichment, the percent of sequencing reads mapping to the Mtb increased to 90.95%

191 et enrichment panel increased the percent of sequencing reads mapping to the Mtb target for all three

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

193 to quickly compute and interactively display sequencing read metrics.

194 ce genome of a female AKV was assembled from sequencing reads obtained from both PacBio long-read and

195 We used sequencing reads of 20-160 kilobases to generate a whole

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

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

198 abase system that links aligned DNA- and RNA-sequencing reads of clinical Pseudomonas aeruginosa isol

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

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

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

202 Most sequencing reads of the VP1 coding region of the SAT1 vi

203 17,676 viral contigs assembled from shotgun sequencing reads of VLP DNAs, we identified viruses that

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

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

206 Aligning sequencing reads onto a reference is an essential step o

207 icient solution for mapping third generation sequencing reads onto assembly graphs of various complex

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

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

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

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

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

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

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

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

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

217 seq can identify cell subtypes with only 100 sequencing reads per cell.

218 8,993 raw sequencing reads-about one million sequencing reads per library-and the pooled sequences we

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

220 lished from an embryo where 92.1% of the PGT sequencing reads possessed a single G insertion that lea

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

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

223 Employing Kraken on unassembled sequencing reads produces a good but variable performanc

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

225 Filtered sequencing reads provided sufficient genome coverage to

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

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

228 At each splice junction suggested by split sequencing reads, read depths of test and control sample

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

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

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

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

233 eomes within either assembled or unassembled sequencing read sets.

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

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

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

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

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

239 circular RNAs (circRNAs) using the number of sequencing reads that support back-splicing junctions (B

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

241 Furthermore, the genomic distribution of sequencing reads, their enrichment at transcription star

242 nized across pipelines to call variants from sequencing reads, there currently exists no standardized

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

244 Longer sequencing reads tip the ratio strongly toward increased

245 sequencing (mWGS) usually starts by aligning sequencing reads to a collection of reference genomes.

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

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

248 find the highest-scoring alignment for real sequencing reads to a linear or graph genome.

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

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

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

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

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

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

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

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

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

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

259 vering the entire process from raw unaligned sequencing reads to cell type annotation.

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

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

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

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

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

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

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

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

268 g, an NGS workflow involves alignment of the sequencing reads to the genome of study, after which the

269 kelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles.

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

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

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

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

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

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

276 The fraction of microbial sequencing reads was greater for the MS group (128.8 PPM

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

278 Sequencing reads were aligned to the National Center for

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

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

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

282 Capture sequencing reads were generated from primary lymphoid tu

283 When these sequencing reads were mapped onto the assembled Unigenes

284 The results demonstrate that 98-100% of sequencing reads were mapped to these liver biomarkers.

285 Sequencing reads were mapped using GSMAPPER, BFAST, and

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

287 Sequencing reads were processed and aligned to the refer

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

289 ord Nanopore, can generate long, error-prone sequencing reads which pose new challenges for fragment

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

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

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

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

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

295 es, for storing polymorphisms or for mapping sequencing reads with greater sensitivity.

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

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

298 fast and RAM-efficient tool to de-duplicate sequencing reads without reference genome.

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

300 rom de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected.