ライフサイエンスコーパス: short-read

1 reads from an assembly of barcoded pools of short reads.

2 ssive influx of genomics data in the form of short reads.

3 nome and thus are difficult to identify with short reads.

4 encing error corrector designed for Illumina short reads.

5 vely studied using a combination of long and short reads.

6 g only a single Nextera Mate Pair library of short reads.

7 umor cells, that can confound analysis using short reads.

8 long reads and Second Generation Sequencing short reads.

9 orm with paired end sequencing for obtaining short reads.

10 use of challenges in aligning and assembling short reads.

11 erful alternative to marker gene set and 16S short reads.

12 constituent peptide fragments identified on short reads.

13 g the results of studies using both long and short reads.

14 nt technologies provide high throughput, but short reads.

15 ity rate and repeat content from unprocessed short reads.

16 t genomes that are difficult to analyze with short reads.

17 improve the homology search performance for short reads.

18 g techniques produce millions to billions of short reads.

19 rimarily being driven by spurious mapping of short reads.

20 y local assembly of unmapped mates of mapped short reads.

21 encing pipelines which routinely match these short reads against reference genomes for contig assembl

22 experiments, a considerable fraction of the short reads align to multiple locations on the reference

23 des the option to use either of two existing short-read aligners, each with different strengths.

24 A-Seq, substantial biases and uncertainty in short read alignment pose challenges for data analysis.

25 Here, we describe RRBSMAP, a short-read alignment tool that is designed for handling

26 a complete transcriptome analysis workflow: short-read alignment, transcript identification/quantifi

27 otein domain-domain interaction network with short read alignments for transcript abundance estimatio

28 lightweight Web application for visualizing short read alignments.

29 by assembling a human genome, de novo, from short reads alone (67x coverage).

30 y to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (d

31 g read regions with the initial insufficient short reads and correct the uncorrected regions in betwe

32 ete open reading frames (ORFs) directly from short reads and identify the coding ORFs, bypassing othe

33 ctrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approac

34 ic analysis tool, MetaPhlAn, on terabases of short reads and provide the largest metagenomic profilin

35 mponents of any given input, i.e., metadata, short reads and quality score strings, are first parsed

36 ementation is among the fastest for indexing short reads and the only one that practically works for

37 It de novo assembles short reads and then maps the assembly against a referen

38 ific Biosciences Iso-Seq long-read, Illumina short-read and deepCAGE (Cap Analysis of Gene Expression

39 trate using simulations, SNP genotyping, and short-read and long-read data how the method improves th

40 ong-read sequencing technology with standard short-read approaches enables more precise and comprehen

41 ion of genetic variants were not detected by short-read approaches, once the alternate allele is sequ

42 Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation e

43 However, short reads are difficult to assemble and often lead to

44 Genomes assembled de novo from short reads are highly fragmented relative to the finish

45 at have a potential to significantly improve short read assemblies.

46 t abundant organisms in the communities, yet short-read assemblies achieved only partial genome cover

47 three-way comparison including the published short-read assembly (SR) constructed for the same indivi

48 With improved short-read assembly algorithms and the recent developmen

49 orona pyxidata, samples that have challenged short-read assembly approaches.

50 ogies produce high coverage of the genome by short reads at a low cost, which has prompted developmen

51 the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investig

52 thylation (ASM) in data from high-throughput short-read bisulfite sequencing.

53 y-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-

54 The ambiguous mapping of short reads by and high cost of current bisulfite sequen

55 Assembly of these short reads can be challenging for genomes and metagenom

56 eq-based gene expression estimates, and that short reads can have a particularly strong impact.

57 y, we used rasbhari to generate patterns for short read classification with CLARK-S.

58 tely, detecting such events from millions of short reads confounded by sequencing errors and RNA edit

59 d mappers have difficulty accurately mapping short reads containing complex variation (i.e. more than

60 assembly-based variant calling, we simulated short reads containing more than 3 million of single nuc

61 HALC aligns the long reads to short read contigs from the same species with a relative

62 sequencing technologies and availability of short read data enable the detection of structural varia

63 (NGS) technologies generate large amounts of short read data for many different organisms.

64 encing (NGS) technologies, a large amount of short read data has been generated.

65 Most of the entropy of short read data lies not in the sequence of read bases t

66 ng sequences cannot be directly used for NGS short read data.

67 haplotype phasing and genotype-calling from short read data.

68 t position-specific nucleotide biases in HTS short read data.

69 on-private state-of-the-art read aligners on short read data.

70 an potentially be useful for the analysis of short reads data from NGS.

71 ew sequencing technologies producing massive short reads data, metagenomics is rapidly growing, espec

72 several errors in contigs assembled from the short-read data alone.

73 han 2 kbp) in combination with high coverage short-read data and, in parallel, by comparing with pare

74 Short-read data from 384 Campylobacter clinical isolates

75 Short-read data from next-generation sequencing technolo

76 , it has become faster and cheaper to obtain short-read data from which to assemble genomes.

77 ge and highly accurate de novo assembly from short-read data is one of the most pressing challenges i

78 However, a major limitation of short-read data is that it is difficult to accurately pr

79 erization of polymorphic Alu insertions from short-read data remains a challenge.

80 However, deep coverage variations in short-read data sets and high sequencing error rates of

81 r annotation of the updated assemblies using short-read data sets was developed and implemented.

82 erited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are re

83 e novo assembly algorithms on four different short-read data sets, all generated by Illumina sequence

84 Furthermore, by combining Illumina short-read data with long reads, we phased both single-n

85 detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algo

86 led ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of in

87 r barcoding strategy and de novo assembly of short-read data.

88 he robust assembly of the virus genomes from short-read data.

89 r identifying structural variants (SVs) from short read datasets are inaccurate.

90 are often fully represented in whole-genome short-read datasets and contribute to inappropriate alig

91 main annotation, the sensitivity of HMMER on short reads declines rapidly.

92 nalysis platform optimized for analysis with short-read deep sequencing.

93 ein domain analysis pipelines are applied to short reads directly or to contigs that are generated us

94 cterized due to challenges with interpreting short-read DNA sequences.

95 The widespread adoption of short-read DNA sequencing as a digital epigenomic readou

96 alanced variants, which we constructed using short-read DNA sequencing data and statistically phased

97 tochondrial DNA abundance using whole-genome short-read DNA sequencing.

98 ls using DNA polymerases and high-throughput short-read DNA sequencing.

99 Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing t

100 s have the capability to produce millions of short reads every day.

101 s) based on long reads for contig formation, short reads for consensus validation, and scaffolding by

102 For error-containing short reads, FragGeneScan finds more prokaryotic coding

103 alysis on NGS datasets with large numbers of short read fragments.

104 We show that short reads from 16S rRNA genes retain sufficient inform

105 reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving ph

106 d on the Burrows-Wheeler transform that maps short reads from a newly sequenced genome to an arbitrar

107 embly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric

108 t these RNA sequences reconstructed from the short reads from each of the pools are mostly close to f

109 Here we develop a method that takes short reads from high-throughput sequencing and outputs

110 s, but the resulting data typically comprise short reads from hundreds of different organisms and are

111 e present a generic approach for integrating short reads from large genomic regions, thus enabling ph

112 90% of the splice junctions are supported by short reads from matched tissues.

113 on from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs

114 em challenging to detect with the relatively short reads from next-generation sequencing (NGS).

115 d metabolic potential, but assemblies of the short reads generated by current sequencing platforms ma

116 the bioinformatic analysis of the relatively short reads generated by second generation sequencing pl

117 Almost all de novo short-read genome and transcriptome assemblers start by

118 (RFA), captures the relationships among the short reads governed by the long read process via a Mark

119 assembles long reads (with low coverage) and short reads has a potential to generate high-quality ass

120 GC detection through short reads has previously been confounded by genomic re

121 Short-read high-throughput RNA sequencing, though powerf

122 Short-read, high-throughput sequencing technology cannot

123 The low sensitivity on short read homology search can lead to inaccurate domain

124 te a scaffold for an assembly generated from short-read Illumina data.

125 ad sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; howev

126 een developed, the problem of assembling the short reads into full-length transcripts remains challen

127 vide satisfactory performance in classifying short reads into their native domain families.

128 vo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of inform

129 iral populations involves assembling the NGS short reads into whole-genome sequences and estimating f

130 However, obtaining a finished genome from short reads is still an open challenge.

131 assembly, which recovers gene segments from short reads, is an important step in functional analysis

132 throughput DNA sequences, but the relatively short read length limits their use in genome assembly or

133 wever, key obstacles such as low throughput, short read length, high error rate, and undetermined bia

134 to multiple sequence ID assignment caused by short read length.

135 -contiguous transcript structure, relatively short read lengths and constantly increasing throughput

136 The relatively short read lengths associated with the most cost-effecti

137 otein databases requires long run-times, and short read lengths can result in spurious hits to unrela

138 copy number variation among individuals and short read lengths generated by HTS technologies.

139 The short read lengths of early Sanger and current next-gene

140 uctural events is challenging because of the short read lengths of second-generation technologies.

141 n, which is a challenging problem because of short read lengths, as well as various sampling biases.

142 structure of the DNA templates is limited by short read lengths.

143 de the large volume of data being generated, short-read lengths and different data types and data for

144 entifying transcriptional units de novo from short reads located all across the genome.

145 ormed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-geno

146 To handle the short reads, LW-FQZip uses a novel light-weight mapping

147 es have been developed for this purpose, but short reads make it a difficult problem in principle.

148 del, we evaluate sites within the arrays for short-read mappability and chromosome specificity.

149 uence to a reference genome using the bowtie short read mapper.

150 Genome resequencing and short read mapping are two of the primary tools of genom

151 Short read mapping is therefore a fundamental component

152 . histolytica genome provide a challenge for short-read mapping, yet we were able to define putative

153 gression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality

154 Short-read massively parallel sequencing has revolutioni

155 econstruct genomes directly from mate-paired short-read metagenomes.

156 reliably detect and quantify target genes in short-read metagenomes.

157 accurately reconstruct BCR repertoires from short read mRNA-seq data.

158 e the entire genome, each of the billions of short reads must be mapped to a reference genome based o

159 S. miltiorrhiza transcriptome have relied on short-read next-generation sequencing (NGS) technology,

160 f genomes have proven difficult to map since short reads of 50-100 base pairs (bps) from these region

161 oftware, configured together in order to map short reads of a genome and call variants.

162 outputs estimates of the true sequences for short reads of DNA or RNA.

163 ined from fungal cultures and for alignable, short reads of environmental amplicons.

164 Our approach is unique in its utilization of short reads only from 16S rRNA genes, not from entire ge

165 ort a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies.

166 is based either on de novo assembly of the (short) reads, or on mapping donor reads to a standard re

167 ntial 50-500% cost cuts) and, interestingly, short reads outperformed long reads for standard analyse

168 quencing of amplicons >500 bp using Illumina short read paired-end sequencing.

169 or genome with high precision from standard, short-read, paired-end sequencing datasets.

170 genotyping and low-coverage sequencing on a short-read platform.

171 ed sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in

172 uencing demand complimenting high-throughput short-read platforms with long-read mapping.

173 , but is still challenging wherever aligning short reads poses ambiguities.

174 oducing high-quality de novo assemblies from short-reads remains challenging, primarily because of th

175 Short reads require a high level of sequence similaritie

176 ion of full length transcripts entirely from short-read RNA sequencing data (RNA-seq) remains a chall

177 ally, there are many existing datasets where short-read RNA sequencing data are available but PCR amp

178 ts adaptive immune receptor repertoires from short-read RNA sequencing data.

179 The availability of high-throughput short-read RNA sequencing technologies provides in-depth

180 ter identifies variable splicing events from short-read RNA-seq data and finds events of high complex

181 Applying GRIT to Drosophila melanogaster short-read RNA-seq, cap analysis of gene expression (CAG

182 e not annotated in GENCODE and are missed by short-read RNA-Seq.

183 Short-read RNAseq is limited in its ability to resolve c

184 iently extract TCR sequence information from short-read scRNA-seq libraries.

185 bed here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs

186 anger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techn

187 New compression techniques tailored to short-read sequence data are needed.

188 technologies, which provide vast amounts of short-read sequence data at relatively low cost.

189 on of finite-state automaton to map Illumina short-read sequence data for individual TcRs to their re

190 The alignment comprises novel, paired short-read sequence data from a single highly inbred lin

191 with a pipeline for the de novo assembly of short-read sequence data from functional selections (ter

192 STR genotyping with short-read sequence data is confounded by (1) the diffic

193 n of mixed infection haplotypes from current short-read sequence data is not consistently possible.

194 we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy.

195 evolution is the collection of time-resolved short-read sequence data.

196 ing in size from 7 bp to 1 kbp compared with short-read sequence data.

197 public browser for the integrated display of short-read sequence-based annotations relative to key su

198 l-length cDNAs are amplified, fragmented and short-read-sequenced.

199 a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer

200 significant improvement in the alignment of short read sequences from immune receptors and that the

201 identification and allelic pair inference to short read sequences, and applied it to data from Illumi

202 ila simulans genome using 142 million paired short-read sequences and previously published data for s

203 nary genetic parameters from a collection of short-read sequences obtained from a mixed sample of ano

204 iome samples using computational analyses of short-read sequences remains a difficult problem.

205 onal time scales linearly with the number of short-read sequences, and is independent of the number o

206 mes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcripto

207 ents from the reference panel to explain the short read sequencing data for a given individual.

208 An accurate genome assembly from short read sequencing data is critical for downstream an

209 researchers with a powerful tool to analyze short read sequencing data.

210 ndently call genotypes at polymorphic sites, short read sequencing often collects haplotypic informat

211 With rapid advances in short read sequencing technologies, sequencing is quickl

212 Our assembly and mapping strategy uses only short read sequencing technology and is applicable to an

213 novel framework for haplotype inference from short read sequencing that leverages multi-single nucleo

214 opment within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of flora

215 put platform prepares barcoded libraries for short-read sequencing and computationally reconstructs l

216 ocesses, but methods such as microarrays and short-read sequencing are unable to describe an entire R

217 n of EVEs has been difficult to resolve with short-read sequencing because they tend to integrate int

218 Accurate typing of HLA genes with short-read sequencing data has historically been difficu

219 However, converting short-read sequencing data into reliable genotype data r

220 Yet profiling STRs from short-read sequencing data is challenging because of the

221 indels of more than a few bases in size from short-read sequencing data remains challenging.

222 h throughput technologies relies on aligning short-read sequencing data, a process that has inherent

223 , such variants are difficult to detect from short-read sequencing data, especially when they exceed

224 n developed for detecting microsatellites in short-read sequencing data, these are limited in the siz

225 three distinctive signals of duplication in short-read sequencing data, we identified 744 duplicated

226 , owing to difficulties in detecting them in short-read sequencing data.

227 o identify structural variants from Illumina short-read sequencing data.

228 imations of error rates for next-generation, short-read sequencing data.

229 s (SBTs), a method for querying thousands of short-read sequencing experiments by sequence, 162 times

230 h-throughput sequencing (ChIP-seq) and other short-read sequencing experiments, a considerable fracti

231 Short-read sequencing has enabled the de novo assembly o

232 d identified over 149,000 SNPs across the 13 short-read sequencing libraries (SRSLs).

233 data currently generated by high-throughput short-read sequencing machines still results in hundreds

234 y of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment

235 Massively parallel, short-read sequencing of mRNA libraries was used to gene

236 been available, the current high-throughput short-read sequencing paradigm is sufficient to obtain a

237 e into fragments whose ends are sequenced on short-read sequencing platforms.

238 detection of structural variants (SVs) from short-read sequencing still poses challenges, particular

239 lows easy manipulation of aligned reads from short-read sequencing technologies (ChIP-seq, FAIRE-seq,

240 Explosive growth of short-read sequencing technologies in the recent years r

241 bstantially higher than the ones produced by short-read sequencing technologies, they can generate de

242 variable and thus difficult to analyze using short-read sequencing technologies.

243 assembly problematic, especially when using short-read sequencing technologies.

244 er from low throughput compared to competing short-read sequencing technologies.

245 y, it has been complementing the widely used short-read sequencing technology by assisting with scaff

246 but repeats are challenging to analyse using short-read sequencing technology.

247 Here, we demonstrate a method to leverage short-read sequencing to obtain long and accurate reads.

248 de physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of S

249 hasing by integrating the data from Illumina short-read sequencing, 10X Genomics linked-read sequenci

250 be sequenced with multi-fold coverage using short-read sequencing.

251 tained in long genomic fragments analyzed by short-read sequencing.

252 s Sulfuricurvum sp. RIFRC-1, via assembly of short-read shotgun metagenomic data using a complexity r

253 memory requirements for de novo assembly of short-read shotgun sequencing data from these complex po

254 an independent dataset generated by the ART short read simulation software and observe that LoQuM ca

255 cy and functional annotation data as well as short read support for the called variant.

256 obbes, a new gram-based program for aligning short reads, supporting Hamming and edit distance.

257 ity of targeted loci, outperforming existing short-read techniques.

258 , with an N50 of 971 kb, using both long and short read technologies.

259 On the other hand, the inexpensive short reads technologies produce accurate but fragmented

260 oon, which promise to outperform the current short-read technologies in terms of throughput.

261 bed sequence, that are currently hidden from short-read technologies.

262 e due to technical difficulties derived from short-read technology.

263 t-generation sequencing technologies produce short reads that are either de novo assembled or mapped

264 hort-Pair increases the accuracy in aligning short reads that are part of remote homologs.

265 quencing technology and produces millions of short reads that contain errors.

266 algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read

267 ChIP-Seq furnishes millions of short reads that, after alignment, describe the genome-w

268 s is indicated by variation in the counts of short-reads that map anomalously to that locus.

269 cessive number of small DNA segments -called short reads- that cause significant computational burden

270 eads with Second Generation Sequencing (SGS) short reads, the accuracy of haplotyping and ASE quantif

271 Compared with short reads, the assemblies obtained from long-read sequ

272 From approximately 1.92 billion short reads, the largest number of differentially expres

273 encing (ChIP-seq) data start by aligning the short reads to a reference genome.

274 approaches that leverage the high quality of short reads to correct errors in long reads.

275 ntification owing to difficulties in phasing short reads to faithfully recover the original strain-le

276 Several programs have been developed to map short reads to genomes in color space.

277 is tools generally rely on accurately mapped short reads to identify somatic variants and germ-line g

278 pecimens, generating 680 million informative short reads to quantitatively characterize the entire tr

279 This bias occurred at the level of aligning short reads to reference genomes to detect variants.

280 can align 10s of billions of base pairs from short reads to the human genome per computer processor d

281 ic variation is identified mainly by mapping short reads to the reference genome or by performing loc

282 riptome analysis is alignment of millions of short reads to the reference genome or transcriptome.

283 ause traditional sequencing methods give too short reads to unambiguously reconstruct chromosomal reg

284 of the efficiency and low cost per base, but short reads typical of NGS only report mRNA fragments co

285 number can be accurately estimated from the short reads typically obtained from high-throughput envi

286 and found that a minimum of 30X coverage of short reads was needed to ensure reliable SNV calling an

287 orithm to predict structural variations from short reads, we report a comprehensive catalog of somati

288 sed GAS typing information directly from the short-read WGS data.

289 ches rapidly produce millions to billions of short reads, which allow pathogen detection and discover

290 curate approach to estimating error rates in short reads, which has the added advantage of not requir

291 s genomes directly from the SLR's underlying short reads, which we refer to as read clouds This enabl

292 ge, particularly for genomes sequenced using short reads, which yield highly fragmented assemblies.

293 ) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data.

294 bal E. coli, 2008-2013, using both long- and short-read whole-genome sequencing.

295 ARK-S, a new software tool that can classify short reads with high precision, high sensitivity and hi

296 This combination of short reads with long-range information represents a pow

297 ate that nanopore long reads are superior to short reads with regard to detection of de novo chromoth

298 cations and underlying sequence variation of short reads within a user-specified distance threshold.

299 ong fragment libraries, to confidently align short reads within repeat regions and enable accurate va

300 ides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normall