ライフサイエンスコーパス: short-read

1 ormation while maintaining the advantages of short reads.

2 e reduced functional signal contained in the short reads.

3 ns of the genome that cannot be mapped using short reads.

4 support for realignment of both RNA and DNA short reads.

5 nerating megabase (Mb)-scale haplotypes with short reads.

6 but most existing methods were designed for short reads.

7 on both assembled sequences and unassembled short reads.

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

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

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

11 ity rate and repeat content from unprocessed short reads.

12 improve the homology search performance for short reads.

13 g techniques produce millions to billions of short reads.

14 rimarily being driven by spurious mapping of short reads.

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

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

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

18 encing error corrector designed for Illumina short reads.

19 the per base error rate is that of Illumina short-reads.

20 pping to 38 Mb of sequence not accessible to short reads, adding sequence in 423 difficult-to-sequenc

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

22 Arioc, a GPU-accelerated short-read aligner, can compute WGS (whole-genome sequen

23 ic pipelines comprising the combination of 7 short-read aligners and 10 variant calling algorithms (V

24 re closely determined by VCAs rather than by short-read aligners.

25 xploit high-concurrency hardware to generate short-read alignments at high speed.

26 nal acceleration, Arioc computes two million short-read alignments per second in a four-GPU system; i

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

28 e genome analysis that is not possible using short reads alone.

29 s, atypical or unusual organisms reported in short-read amplicon sequencing studies and that are not

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

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

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

33 fic region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for

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

35 ter and uses less memory than all comparable short-read and long-read analysis tools.

36 s the incorporation of information both from short-read and long-read DNA sequencing technologies.

37 nkedSV can detect SVs missed by conventional short-read and long-read sequencing approaches, and may

38 High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-

39 we analyze the MYCN amplicon structure using short-read and Nanopore sequencing and its chromatin lan

40 ese long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to id

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

42 However, these short-read approaches fail to give a complete picture of

43 the advantages of Linked-Reads over standard short-read approaches for reference-based analysis.

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

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

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

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

48 reads, which further improves the quality of short-read assemblies.

49 bacterial genomes as compared to fragmented short-read assemblies.

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

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

52 ences that were not recovered using standard short-read assembly approaches.

53 genes, compared to only seven alleles in the short-read assembly.

54 nome improves the contig N50 of the previous short-read based buffalo assembly more than a thousand-f

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

56 bly of the giant panda is available, current short read-based assemblies are limited to moderately si

57 obial community, and provide a comparison to short read-based methods.

58 Short-read bisulfite sequencing and long-read PacBio seq

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

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

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

62 , alpha (~340 bp) and CapA (~1,500 bp), from short-read clustering of sequencing datasets from S. bol

63 enomic studies of microbial communities, the short reads come from mixtures of genomes.

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

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

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

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

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

69 nally robust approach that uses whole genome short read data to determine the occupation status at al

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

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

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

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

74 O. nubilalis mtDNA assembly from unenriched short-read data analogously showed 77 variant sites.

75 a growing need for timely computation in the short-read data analysis toolchain.

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

77 t multisample, colored de Bruijn graphs from short-read data for all samples, align long-read-derived

78 es are not designed to incorporate long- and short-read data from mother-father-child trios, and ther

79 y can be pursued either by incorporating the short-read data into the early phase of assembly, during

80 notyping of structural variations (SVs) from short-read data is a long-standing area of development i

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

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

83 equencing have made HLA typing from standard short-read data practical.

84 identification of structural variants using short-read data remains challenging.

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

86 it is challenging to search a repository of short-read data using relational logic and to apply that

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

88 better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do n

89 smission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and d

90 rate is to combine long reads with low-cost short-read data, which currently have an error rate belo

91 s, Salmonella enterica, and Escherichia coli short-read datasets, we demonstrate that within-species

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

93 NNs) for filtering small genomic variants in short-read DNA sequence data.

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

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

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

97 challenging both de novo assembly, in which short reads do not capture the long-range context requir

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

99 e, which incorporates long-read assembly and short-read error correction, to assemble closed bacteria

100 et sites are detectable in gene bodies where short-reads fail to uniquely align.

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

102 lease cut site information from sequences of short-read fragments and produces single-locus binding e

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

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

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

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

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

108 90% of the splice junctions are supported by short reads from matched tissues.

109 icHET works on short reads from multiple samples from any organism with

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

111 ut genome as a reference for the assembly of short reads from six Juglans species and several intersp

112 nome to the de Bruijn graph constructed from short reads generated from the same genome.

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

114 which ~40% are invisible to high specificity short-read genotyping approaches.

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

116 ead technologies (aka read cloud or barcoded short-reads) have revived interest in short-read technol

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

118 Combining short-read Illumina and long-read Oxford Nanopore sequen

119 This study employed both short-read Illumina RNA sequencing and long-read Pacific

120 However, the favored approaches such as short-read Illumina RNA sequencing are giving way to lon

121 g as single reads, as well as for generating short-read Illumina sequences.

122 ects methylation with accuracy comparable to short-read Illumina sequencing but with long-range epige

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

124 equencing' technologies produce a relatively short read length and demand a reverse-transcription ste

125 her popular sequencing technologies is their short read length relative to the lengths of (common) ge

126 limited by the loss of native modifications, short read length, high input requirements, low yield or

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

128 iants remains an unsolved problem due to the short-read length of common sequencing data.

129 scriptome annotations have largely relied on short read lengths intrinsic to the most widely used hig

130 iments highlighted that in Hi-C studies with short read lengths, mHi-C rescued multi-reads can emulat

131 to compensate the information loss owing to short read lengths.

132 gh molecular weight DNA, we produce barcoded short-read libraries.

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

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

135 However, the massive size of short reads makes de novo transcripts assembly an algori

136 Short read mapping is therefore a fundamental component

137 s is the genomic signal track constructed by short read mapping to a particular genome assembly.

138 Short-read massively parallel sequencing has revolutioni

139 e challenge of assembling viral genomes from short-read metagenomes.

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

141 The annotation of short-reads metagenomes is an essential process to under

142 recise distribution of any protein domain in short-reads metagenomes.

143 Short-read metagenomic sequencing and de novo genome ass

144 remain substantially higher than those from short-read methods, we demonstrate the substantial benef

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

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

147 Combining short-read (N = 127) and long-read re-sequencing (N = 31

148 n unbiased assessment of community function, short reads need to be mapped directly to a gene or prot

149 Although established short-read NGS technologies are known to provide highly

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

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

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

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

154 in use today produce either highly accurate short reads or less-accurate long reads.

155 opulation response involves a trade-off: For short read-out times, stimulus estimates are unreliable

156 nce of 269 Mb that was assembled by Illumina short reads, PacBio long reads and high-confidence (Hi-C

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

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

159 chnologies there remains a trade-off between short-read platforms, having limited ability to sequence

160 , the tagged reads are sequenced on standard short-read platforms.

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

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

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

164 xity associated with multimapping reads from short-read RNA sequencing experiments, and we show that

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

166 identification of full-length transcripts in short-read RNA-Seq data, which encourages the developmen

167 h to understanding transcript diversity from short-read RNA-Seq data.

168 Both short-read RNA-seq-based HLA typing and BCR/TCR repertoi

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

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

171 pecific genome studies over large numbers of short read samples.

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

173 low-cost, high-accuracy, and high-throughput short-read second-generation sequencer to generate over

174 closely related elements such as HERV-K from short read sequence data.

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

176 Here, we used a combination of long- and short-read sequence data of Klebsiella pneumoniae isolat

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

178 onstructed within-host viral haplotypes from short-read sequence data.

179 ysis of plasmid epidemiology based solely on short-read sequence data.

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

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

182 apply Paragraph at scale to a cohort of 100 short-read sequenced samples of diverse ancestry.

183 g long single-molecule real-time reads, with short read sequences (Illumina) for refinement, and cons

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

185 The ability to detect genes in short read sequences is dependent on pre- and post-seque

186 the first time the clinical WGS analysis of short-read sequences has been used successfully to ident

187 that, across samples, 58.3% of the 4,726,023 short-read sequences matching with a GH domain-containin

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

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

190 algorithm to identify and correct errors in short read sequencing data.

191 otypic inducibility of meropenem resistance, short read sequencing was performed using an Illumina Ne

192 for further analysis, including whole-genome short-read sequencing and additional antimicrobial susce

193 ndividual organisms compared to conventional short-read sequencing and assembly methods.

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

195 s insertions are often missed using standard short-read sequencing approaches and long-read sequencin

196 However, bacterial genomes assembled from short-read sequencing are often fragmented.

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

198 ormat addresses rising DNA storage costs for short-read sequencing by aligning reads to a reference g

199 t methods for determining RNA structure with short-read sequencing cannot capture most differences be

200 equencing provides long-range information on short-read sequencing data by barcoding reads originatin

201 r the analysis of large-scale, low-depth and short-read sequencing data from non-model organisms with

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

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

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

205 g methods for detecting repeat expansions in short-read sequencing data require predefined repeat cat

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

207 Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity

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

209 tive MGEs and their insertion sites by using short-read sequencing data.

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

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

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

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

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

215 nes in the gut, technological limitations of short-read sequencing have precluded linking bacterial t

216 of global transcriptomes using conventional short-read sequencing is challenging due to the insensit

217 Without adequate depth, both long-read and short-read sequencing may not detect the variants presen

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

219 that targeting of 16S variable regions with short-read sequencing platforms cannot achieve the taxon

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

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

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

223 We used long- and short-read sequencing technologies to investigate end pr

224 his problem has been extensively studied for short-read sequencing technologies, but current solution

225 equately assembled or aligned using standard short-read sequencing technologies, preventing researche

226 length with an accuracy approaching that of short-read sequencing technologies, these platforms have

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

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

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

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

231 man genome is limited by the read lengths of short-read sequencing technologies.

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

233 ally important genomic regions overlooked by short-read sequencing that are largely resolved by long-

234 CCS method matches or exceeds the ability of short-read sequencing to detect small variants and struc

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

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

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

238 ithin cell extracts prior to DNA extraction, short-read sequencing, and assembly using exemplars from

239 limited by reliance on DNA fragmentation and short-read sequencing, cannot provide information about

240 at would impede accurate m(6)A mapping using short-read sequencing, here we profile m(6)A within the

241 scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequenc

242 ower coverage, and are more error prone than short-read sequencing, these methods continue to be supe

243 emarcate the boundaries of isoforms based on short-read sequencing, with higher efficiency and lower

244 n of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater

245 t can potentially address the limitations of short-read sequencing.

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

247 ding in dark genomic regions inaccessible by short-read sequencing.

248 files known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data.

249 he reference genome, a significant number of short reads still remain unmapped and are often excluded

250 Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, opt

251 L1Hs insertions that were absent in previous short-read studies (90/203).

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

253 fective means for leveraging SV catalogs for short-read SV genotyping experiments.

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

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

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

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

258 inly on the compression of data generated by short-read technologies.

259 rcoded short-reads) have revived interest in short-read technology as a viable approach to understand

260 solve in reference genomes and genotype with short-read technology.

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

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

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

264 h support and instead rely on inference from short reads that do not span the full length of the isof

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

266 t commonly used sequencing platforms produce short reads that only span up to two exon junctions per

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 during the read correction step, or by using short reads to "polish" the consensus built from long re

274 informatic approaches allow for the barcoded short reads to be associated with their original long mo

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

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

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

278 t tools have shown great accuracy in mapping short reads to the reference genome, a significant numbe

279 GS) applications start with mapping/aligning short reads to the reference genome, with the aim of ide

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

281 overlaps with variants and adversely impacts short-read variant calling.

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

283 rangements and oncogenic translocations from short-read WGS data.

284 with full-length super-reads assembled from short reads, which further improves the quality of short

285 h-quality second-generation sequencing (SGS) short reads, which is referred to as hybrid error correc

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

287 ed interspersed segmental duplications using short read whole genome sequencing datasets.

288 Successful diplotyping with short read whole genome sequencing generally requires ei

289 human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; however,

290 nd deletions, have not proved tractable with short-read whole genome sequencing.

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

292 Short-read whole-genome sequencing data are often applie

293 Here, we combine long- and short-read whole-genome sequencing data with recent asse

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

295 s diversity has largely been uncovered using short-read whole-genome sequencing.

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

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

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

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