ライフサイエンスコーパス: long-read

1 ome assembler that works with both short and long reads.

2 highly accurate short reads or less-accurate long reads.

3 advantage of linkage information provided by long reads.

4 accurately discover introns, especially with long reads.

5 ly outperforming assembly with less-accurate long reads.

6 ent of sequencing technologies that generate long reads.

7 generating paired-end, mate-pair, linked and long reads.

8 tate-of-the-art error-correction methods for long reads.

9 benefit of performing transcript assembly on long reads.

10 t reads to "polish" the consensus built from long reads.

11 (A1), which was scaffolded using linked and long reads (A2) and then merged with the previously publ

12 dividual chromatin fibers, a single-molecule long-read accessible chromatin mapping sequencing assay

13 ) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in

14 ped to segmental duplications using existing long-read aligners and leverages paralogous sequence var

15 pped reads with high confidence for multiple long-read aligners including Minimap2 (74.3-90.6%) and B

16 Long-read alignments and Hi-C linkage between contigs su

17 nd, for each long read, references the other long reads' alignments to find the most accurate alignme

18 Using qPCR and long-read amplicon deep sequencing, we detected subpopul

19 reads can greatly improve the sensitivity of long-read analyses.

20 ss memory than all comparable short-read and long-read analysis tools.

21 De novo assembly of long reads and cytogenetics confirmed this species-speci

22 as assembled by Illumina short reads, PacBio long reads and high-confidence (Hi-C) data.

23 reads to the reference genome, but accurate long reads and linked reads now enable us to construct a

24 oving low-quality sequences using linked and long reads and merging of assemblies.

25 new methods to handle the high error rate of long reads and offers the ability to work with full-leng

26 logies obsolete with its ability to generate long reads and provide portability.

27 s (chimpanzee, gorilla, and orangutan) using long-read and 10x Genomics linked-read sequence data for

28 Together with new long-read and direct RNA-seq technologies and better com

29 Without adequate depth, both long-read and short-read sequencing may not detect the v

30 an Illumina shotgun library, Oxford nanopore long reads, and chromosome conformation capture for long

31 Here we present long-read annotation (LoReAn) software, an automated ann

32 However, long-read applications are still constrained by their hi

33 e limit for perfect correction, beyond which long reads are too error-prone to be corrected by these

34 These long reads are used to construct an assembly (i.e. the s

35 discover the tandem repeat patterns from the long-reads are either inefficient or lack sensitivity.

36 enome assembly, we present Shasta, a de novo long-read assembler, and polishing algorithms named Marg

37 Existing long-read assemblers require thousands of central proces

38 eteness and contiguity than state-of-the-art long-read assemblers.

39 remains difficult even for state-of-the-art long-read assemblers.

40 y genomes using published reference genomes, long read assemblies and k-mer-based methods to contextu

41 Recent long-read assemblies often exceed the quality and comple

42 Here, we present Flye, a long-read assembly algorithm that generates arbitrary pa

43 e genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat

44 The long-read assembly also identifies 94 antimicrobial resi

45 ur workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to a

46 It paves the way for population-scale long-read assembly in future.

47 tors, scientists, and students in performing long-read assembly of bacterial and bacteriophage genome

48 Finally, we show that long-read assembly of human microbiomes enables the disc

49 ore accurate C. elegans genome, we performed long-read assembly of VC2010, a modern strain derived fr

50 ngth of 7.7 million bases (Mb) directly from long-read assembly, compared to those of 1.04 Mb for B73

51 held true, the relatively high error rate of long reads, averaging 8-15%, has made it challenging to

52 ere we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and tra

53 of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris.

54 The FLAS corrected long reads can be assembled into contigs of 13.1-29.8% l

55 rror-prone third-generation sequencing (TGS) long reads can be corrected by the high-quality second-g

56 Using BulkVis, we find long reads can be incorrectly divided by MinKNOW resulti

57 The ability to assemble these long reads can greatly improve the sensitivity of long-r

58 is a new method, specifically developed for long reads, capable of mapping a long-read metagenome to

59 ted annotation pipeline utilizing short- and long-read cDNA sequencing, protein evidence, and ab init

60 Here, we provide the detailed protocol for long-read ChIA-PET that includes cell fixation and lysis

61 improved the original approach by developing long-read ChIA-PET, in which the length of the paired-en

62 ession, lossy compression of quality values, long read compression and random access.

63 ew method designed specifically for aligning long reads contaminated by a high level of errors.

64 Additionally, we use long-read DART-seq to gain insights into m(6)A distribut

65 hm, Winnowmap, using both simulated and real long-read data and compared it to a state-of-the-art lon

66 However, the tools for aligning long-read data and detecting SVs have not been thoroughl

67 Improvements in long-read data and scaffolding technologies have enabled

68 Long-read data from the MinION produced an assembly that

69 We generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the

70 odium falciparum experimental crosses, using long-read data on the parents to inform reconstructions

71 require relatively high coverages of costly long-read data to produce high-quality assemblies.

72 iously unknown rumen species, assembled from long-read data.

73 Across multiple whole-genome long-read datasets, DuploMap aligned an additional 8-21%

74 correction on two downstream applications of long reads: de novo assembly and resolving haplotype seq

75 We used long-read, deep-sequenced data of full-length HCV envelo

76 from short-read data for all samples, align long-read-derived haplotypes and multiple reference data

77 Here, we assessed MinION long-read-derived sequences for feasibility concerning:

78 By combining long-read DNA sequencing and Hi-C, we assembled the sex-

79 Third-generation long-read DNA sequencing technologies are increasingly u

80 Recent advances in long-read DNA sequencing technologies, specifically Nano

81 tion of information both from short-read and long-read DNA sequencing technologies.

82 Single-molecule long-read DNA sequencing with biological nanopores is fa

83 Using synthetic biology tools combined with long-read DNA sequencing, we optimize productivity by 50

84 A survey of 132 MRSA genomes assembled from long reads enabled detailed characterization of an outbr

85 roduce HALC, a high throughput algorithm for long read error correction.

86 f accuracy gain with respect to the original long read error rate.

87 a lack of standardized assessments for these long-read error-correction methods.

88 We also report high accuracy for long reads even at relatively low coverage (25x-30x).

89 s cerevisiae, Arabidopsis thaliana and human long reads, FLAS can achieve 22.0-50.6% larger throughpu

90 Here we report an improved long-read genome assembly for P. dactylifera that is 772

91 We then performed long-read genome sequencing and identified a large GGC r

92 technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%

93 ror correction methods for these error-prone long reads have been developed to date.

94 The third generation PacBio long reads have greatly facilitated sequencing projects

95 Short- and long-read high-throughput sequencing of DNA and RNA demo

96 r allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associat

97 nd a large proportion of base pairs in these long reads is incorrectly identified.

98 and that population-level resequencing using long reads is likely to provide novel insight into the e

99 me for Tripsacum dactyloides generated using long-read Iso-Seq data was used to characterize independ

100 We used long-read isoform sequencing combined with a novel analy

101 loid genotype using a strategy that combined long-read length sequencing with chromosome conformation

102 generation DNA sequencing method due to very long read lengths, ability to detect methylated bases, a

103 Though capable of long read lengths, SMS platforms currently suffer from l

104 d data and compared it to a state-of-the-art long read mapper, Minimap2.

105 We introduce lordFAST, a novel long-read mapper that is specifically designed to align

106 ficantly faster than the state of the art in long read mapping.

107 uploMap, designed to improve the accuracy of long-read mapping in segmental duplications.

108 h high sequence identity pose challenges for long-read mapping.

109 veloped for long reads, capable of mapping a long-read metagenome to a comprehensive RefSeq database

110 present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneve

111 oratory and bioinformatics workflows using a long-read nanopore sequencer (MinION) for Y. pestis (6.5

112 To address these gaps, we use long-read nanopore sequencing and assemble the genomes o

113 This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidifo

114 We used long-read nanopore sequencing to capture 238,490 SVs in

115 Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG meth

116 Here, we report the use of long-read nanopore sequencing to simultaneously sequence

117 Using long-read nanopore sequencing we show that, with an aver

118 Long-read next-generation amplicon sequencing shows prom

119 For the projects with long reads only, it is challenging to make correction wi

120 -cell strand sequencing(1,2) with continuous long-read or high-fidelity(3) sequencing data.

121 We assess how well long-read or linked-read technologies resolve these regi

122 he number of stochastic spikes is small; for long read-outs, estimates are biased because they lag be

123 ole-exome (93% accuracy) Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data (

124 Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the

125 ly, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing was conducted on faecal

126 Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to

127 Here we develop a new approach that uses long-read PacBio sequencing to determine the sequences o

128 TideHunter works with noisy long-reads (PacBio and ONT) at error rates of up to 20%

129 id assembly using accurate Illumina data and long-read Pacific Biosciences (PacBio) data from all rel

130 both short-read Illumina RNA sequencing and long-read Pacific Biosciences (PacBio) isoform sequencin

131 tifs or long-range structural variation, and long-read platforms, which tend to have lower accuracy a

132 put sample type and is more common in 'ultra-long' read preparations.

133 tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Na

134 can reduce the cost of genome sequencing and long reads produced from these devices can improve the c

135 The long-read property is exploited to characterize, using n

136 Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical map

137 then constructs a contig graph and, for each long read, references the other long reads' alignments t

138 In addition, FLAS also uses the corrected long-read regions to correct the uncorrected ones to fur

139 However, not all single-molecule long reads represent full transcripts due to incomplete

140 ing using chemical modifications with direct long-read RNA sequencing and machine learning to detect

141 th transcripts from ten different tissues by long-read RNA sequencing.

142 We also briefly evaluated its performance in long-read RNA-seq analysis, by sequencing a mixture of h

143 Specifically, we examine both short- and long-read RNA-seq technologies, 39 analysis tools result

144 gorithm of MECAT, to achieve high-throughput long-read self-correction while keeping MECAT's fast spe

145 This is the first long-read sequence assembly of the horse MHC class II re

146 MinION long-read sequence data also facilitated the elucidation

147 uman structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen hum

148 ng approximately 6.5 terabases of short- and long-read sequence data from 283 ruminant cattle.

149 Using long-read sequence data we obtained complete sequences o

150 Using long-read sequence data, we reconstruct the structure an

151 -2,) bla (KPC-3), and bla (NDM-1)) were also long-read sequenced, and their carbapenemase-encoding pl

152 fficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form lo

153 he Oxford Nanopore Technologies (ONT) MinION long-read sequencer for routine WGS by sequencing the re

154 re broadly, SMURF-seq expands the utility of long-read sequencers for read-counting applications.

155 of human RNAs and RNA Sequins with nanopore long-read sequencers.

156 vo assembly of a human genome using nanopore long-read sequences has been reported, but it used more

157 curacy of L1EM on simulated data and against long read sequencing from HEK cells.

158 Long read sequencing technologies such as Oxford Nanopor

159 riptomes and metagenomes from both short and long read sequencing technologies.

160 With RACE, molecular cloning, and long read sequencing, we found a number of novel SNX19 t

161 In this study, using long read sequencing, we sequenced four Indian-origin rh

162 Our results were comparable in quality to long read sequencing.

163 e represent megabase inversions confirmed by long read sequencing.

164 Long-read sequencing (LRS) can overcome these limitation

165 Long-read sequencing (LRS) has become a standard approac

166 Long-read sequencing (LRS) has become increasingly popul

167 amic lytic transcriptome of BoHV-1 using two long-read sequencing (LRS) techniques, the Oxford Nanopo

168 ferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq), for long-range mappin

169 oped a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-seq) technology, which enable

170 Our findings show that long-read sequencing allows for substantially more accur

171 ojects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing,

172 We used PacBio long-read sequencing and chromosome conformation capture

173 Long-read sequencing and improved mapping of repeats sho

174 Using long-read sequencing and microscopic approaches, we have

175 hinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding appro

176 Long-read sequencing and novel long-range assays have re

177 tic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology.

178 quality SV callsets from short-, linked- and long-read sequencing and optical mapping.

179 Rapid development in long-read sequencing and scaffolding technologies is acc

180 We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic my

181 Here we incorporated long-read sequencing and state-of-the-art scaffolding pr

182 ool samples that are suitable for downstream long-read sequencing applications.

183 orkflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiolo

184 tandard short-read sequencing approaches and long-read sequencing approaches can significantly improv

185 ct SVs missed by conventional short-read and long-read sequencing approaches, and may resolve negativ

186 inical setting, we develop and demonstrate a long-read sequencing based assay.

187 Long-read sequencing can overcome the weaknesses of shor

188 rotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epige

189 Long-read sequencing coupled with bioinformatics tools e

190 For this, we generated PacBio long-read sequencing data and assembled a novel, high-qu

191 n of disease-relevant STRs from whole-genome long-read sequencing data on patients with undiagnosed d

192 sing raw electric signals of Oxford Nanopore long-read sequencing data, we design DeepMod, a bidirect

193 Using PacBio long-read sequencing data, we identified L1Hs insertions

194 s sequences from amplified tandemly repeated long-read sequencing data.

195 infer normal ranges of 432,604 STRs using 21 long-read sequencing datasets on human genomes, and buil

196 Long-read sequencing demonstrated global dissemination o

197 all, our findings demonstrate the utility of long-read sequencing for hospital surveillance and for c

198 t structures, highlighting the importance of long-read sequencing for obtaining phase information.

199 Long-read sequencing from Pacific Biosciences and NGS ba

200 Although long-read sequencing has been applied successfully to th

201 Single-molecule long-read sequencing has been used to improve mRNA isofo

202 Although long-read sequencing improves this issue, it is not amen

203 opore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for b

204 The method will facilitate the use of long-read sequencing in research and in the clinic.

205 s are known to provide highly accurate data, long-read sequencing is still needed to resolve highly-r

206 Long-read sequencing makes it possible to robustly assig

207 We use long-read sequencing methods and modern scaffolding tech

208 gher efficiency and lower cost than existing long-read sequencing methods.

209 These findings highlight the need for long-read sequencing of cancer genomes for the precise a

210 genome-wide TE bioinformatics, we performed long-read sequencing of cDNAs from Arabidopsis (Arabidop

211 Single-molecule long-read sequencing of chromatin stencils enabled nucle

212 Second, we performed long-read sequencing of the sheep microbiome and applied

213 High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a

214 resolve these shared sequences, we performed long-read sequencing on a subset of isolates and generat

215 ad Illumina RNA sequencing are giving way to long-read sequencing platforms better suited to interrog

216 th short reads, the assemblies obtained from long-read sequencing platforms have much higher contig c

217 and Nano-OTS, two novel, amplification-free, long-read sequencing protocols for detection of gRNA-dri

218 Amplification-free long-read sequencing reveals Cas9 cleavage sites in vitr

219 Recent advances in long-read sequencing solve inaccuracies in alternative t

220 nce-resolved SV catalogs generated by recent long-read sequencing studies.

221 Here, we exploit a single-molecule long-read sequencing technique and develop an open-sourc

222 Current long-read sequencing technologies can provide valuable l

223 New long-read sequencing technologies can sequence the entir

224 Current long-read sequencing technologies display a tendency tow

225 Linked-read or long-read sequencing technologies from 10x Genomics, Pac

226 Current long-read sequencing technologies have challenging error

227 Long-read sequencing technologies have contributed great

228 Long-read sequencing technologies have substantially imp

229 Emerging long-read sequencing technologies promise to improve the

230 Although long-read sequencing technologies such as Pacific Biosci

231 Long-read sequencing technologies will soon permit the r

232 Using long-read sequencing technologies, we provide a high-qua

233 refore used a combination of single-molecule long-read sequencing technology and polyadenylation site

234 We describe a method that adds long-read sequencing to a mix of technologies used to as

235 e FcgammaR diversity in 48 MCMs using PacBio long-read sequencing to identify novel alleles of each o

236 ng a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transc

237 We combine long-read sequencing with a Hi-C-based proximity guided

238 /repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outc

239 ditional Culex pipiens mosquitoes using PCR, long-read sequencing, and screening of existing metageno

240 eres of Drosophila melanogaster by combining long-read sequencing, chromatin immunoprecipitation for

241 genomic region and, using third generation, long-read sequencing, we identified a 120 kb insertion i

242 With long-read sequencing, we obtained chromosome-level genom

243 cancer-related genes detectable only through long-read sequencing.

244 ons in gene copy number, which we confirm by long-read sequencing.

245 r and nucleotide composition, as revealed by long-read sequencing.

246 genomes for V. cholerae O139, obtained using long-read sequencing.

247 kedSV identifies SVs missed by high-coverage long-read sequencing.

248 is thaliana based on sequence enrichment and long-read sequencing.

249 s targeted RNA capture with third-generation long-read sequencing.

250 Prunus dulcis cv. Texas combining short- and long-read sequencing.

251 by using single-cell DNA template strand and long-read sequencing.

252 a human clinical sample by high-throughput, long-read sequencing.

253 Here, we apply a suite of long-read, short-read, strand-specific sequencing techno

254 Advances in long-read single molecule sequencing have opened new pos

255 We have developed an approach using long-read single-molecule real-time (SMRT) sequencing th

256 r for gentle and efficient purification with long-read single-molecule real-time sequencing.

257 Long-read single-molecule sequencing, Hi-C sequencing, a

258 Over the past decade, long-read, single-molecule DNA sequencing technologies h

259 Long-read, single-molecule PacBio sequencing allows the

260 Long-read, single-molecule sequencing platforms hold gre

261 iae and Piromyces finnis were assembled with long-read, single-molecule technology.

262 recently developed barcoding-based synthetic long read (SLR) technologies have already found many app

263 nscriptome of C. elegans Taking advantage of long reads spanning the full length of mRNA transcripts,

264 By adding long-read-specific optimizations to Scallop, we develope

265 correct it with the aligned contig regions (long read support based validation approach).

266 enome sequence data from three samples using long-read SV calls as the truth set, and then apply Para

267 rm is most commonly used for sequencing, but long-read technologies are now becoming available that s

268 Long-read technologies can potentially solve such proble

269 rce allocation reference to the community as long-read technologies continue to mature.

270 Although emerging long-read technologies have enabled ETR assemblies, the

271 Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphe

272 However, compared to long-read technologies, the cost per base to sequence is

273 read sequencing that are largely resolved by long-read technologies.

274 en 90% and 95% of variants supported by each long-read technology also supported by the other.

275 g internal references generated by synthetic long-read technology, allowing us to evaluate high-throu

276 In this study, we established a long-read technology-based WGS screening program of all

277 We present long-read Tet-assisted pyridine borane sequencing (lrTAP

278 le real-time (SMRT) sequencing that produces long reads that allow us to obtain detailed and accurate

279 fic Biosciences and Oxford Nanopore generate long reads that can potentially address the limitations

280 eration sequencing technologies can sequence long reads that contain as many as 2 million base pairs.

281 additional alignments from MECAT prealigned long reads to improve the correction throughput, and rem

282 , we developed Scallop-LR, a reference-based long-read transcript assembler.

283 -Seq Analysis and StringTie, indicating that long-read transcript assembly by Scallop-LR can reveal a

284 This drives a need for long-read transcript assembly.

285 ology gene predictions as well as short- and long-read transcriptomics to generate highly complete ge

286 xhibit coordination, showcasing the need for long-read transcriptomics.

287 es (ONT) sequencing technologies can produce long-reads up to tens of kilobases, but with high error

288 Short and long reads were subjected to de novo hybrid assembly.

289 age and rapidly assembled haplotypes for two long-read WGS data sets on which other methods struggled

290 Linked-read sequencing generates synthetic long reads which are useful for the detection and analys

291 rence of haplotypes and genotypes from noisy long reads, which we term diplotyping.

292 Long-read whole genome sequencing was performed using Pa

293 cation and IGH allelic exclusion, we perform long-read whole-genome and transcriptome sequencing alon

294 Short- and long-read whole-genome sequencing highlighted a duplicat

295 Finally, using a combination of short- and long-read whole-genome sequencing, we found no significa

296 targeted DNA double-strand breaks (DSBs) and long-read whole-genome sequencing, we show that a single

297 Access to deep and accurate long reads will facilitate prediction of key beneficial

298 ons do not always successfully generalize to long reads with high indel error rates.

299 a very low overall error rate is to combine long reads with low-cost short-read data, which currentl

300 SMRT sequencing combines long reads with sufficient depth for many phylogenetic a