ライフサイエンスコーパス: long-read

1 ategies aimed directly at fully subassembled long reads.

2 digms to cope with combinations of short and long reads.

3 quality of short reads to correct errors in long reads.

4 d on molecular cloning and that produce very long reads.

5 a need for novel assembly algorithm for the long reads.

6 recovered in the C. elegans genome using the long reads.

7 le tool for upgrading de novo assembly using long reads.

8 -genome Pacific Biosciences RS II Continuous Long Reads.

9 es when the original data are augmented with long reads.

10 the CABOG assembler, which was designed for long reads.

11 ve been deeply sequenced with both short and long reads.

12 ty Illumina paired-end reads mapped onto the long reads.

13 It can handle long reads (50-100 nt) and can exploit paired-read infor

14 We present AGILE (AliGnIng Long rEads), a hash table based high-throughput sequence

15 LR (single-molecule modification analysis of long reads), a novel framework for single molecule-level

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

17 However, the choice of long-read aligners effective in terms of both performanc

18 mpact data summary format for both short and long read alignments that enables the anonymization of c

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

20 n indirect inference methods, e.g. assembly, long reads allow direct inference of satellite higher or

21 The long reads also enable efficient phasing of genetic vari

22 lification of VDJ rearrangements followed by long read amplicon sequencing spanning the VDJ junctions

23 ort reads that minimizes the edit score to a long read and extending corrected regions by local assem

24 ridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial as

25 also show that our algorithms can deal with long reads and deep read coverage effectively and accura

26 pe phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing

27 r, these approaches require high coverage by long reads and remain expensive.

28 s by integrating Third Generation Sequencing long reads and Second Generation Sequencing short reads.

29 We expect that, based upon long-read and high-fidelity next-generation sequencing t

30 and GM12892) by using a Pacific Biosciences long-read approach complemented with Illumina 101-bp seq

31 iguous and complete than alternate short- or long-read approaches.

32 However, so far long reads are characterized by a high error rate, and a

33 We demonstrate that nanopore long reads are superior to short reads with regard to de

34 sing both the assembled contigs and original long reads as input, BIGMAC first breaks the contigs at

35 we follow with assembly using off-the-shelf long-read assemblers.

36 using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical map

37 ned with computational tools for metagenomic long-read assembly, variant calling and haplotyping (Nan

38 HINGE was evaluated on the long-read bacterial data sets from the NCTC project.

39 The third generation PacBio SMRT long reads can effectively address the read length issue

40 tagenomic assemblies with the original input long reads can result in quality improvement.

41 The HALC corrected long reads can thus result in 11.4-60.7% longer assemble

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

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

44 The method combines deep, long-read chromatin immunoprecipitation-sequencing (ChIP

45 ly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 eu

46 is approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated duri

47 human gut microbiome using TruSeq synthetic long reads combined with computational tools for metagen

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

49 The sequence accuracy of the MinION long-read contigs ( approximately 98%) was improved usin

50 Our long-read correction achieves >99.9% base-call accuracy,

51 By utilizing synthetic long-read data (longer than 2 kbp) in combination with h

52 Analysis of long-read data also revealed thousands of species whose

53 ulations, SNP genotyping, and short-read and long-read data how the method improves the accuracy of g

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

55 The long-read data revealed multiple (probably dozens of) cl

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

57 Long distance PCR coupled with long-read direct sequencing was employed to sequence the

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

59 Through long-read DNA sequencing, we obtained a gap-free genome

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

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

62 for accurate assembly, and state-of-the-art long-read error-correction methods use de Bruijn Graphs.

63 ng the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consens

64 and, interestingly, short reads outperformed long reads for standard analyses.

65 Here, we use single-molecule sequencing long reads from Pacific Biosciences (PacBio) to determin

66 e the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing inf

67 ere an automated approach to finishing using long-reads from the Pacific Biosciences RS (PacBio) plat

68 , that takes advantage of Pacific Bioscience long-reads from whole-genome sequencing datasets.

69 e strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and dropl

70 struction, specifically developed to analyze long read (>100 bp) NGS data.

71 ce can be applied to both short (<75 bp) and long reads (>/= 75 bp).

72 a-read discordance and soft-clipped tails of long reads (>10,000 bp) to identify structural variants.

73 onally evaluated a collection of new de novo long-read haploid assemblies and conclude that although

74 Here we describe statistically aided, long-read haplotyping (SLRH), a rapid, accurate method t

75 However, at present, long reads have an error rate as high as 10-15%.

76 While MinION long reads have an error rate substantially higher than

77 The biggest challenge today is that long reads have relatively high error rates, currently a

78 ation of viral vector integration sites from long read high-throughput sequencing.

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

80 expression-profiling strategy that utilizes long-read, high-throughput sequencing to capture the inf

81 ue attributes of Pacific Biosciences Iso-Seq long-read, Illumina short-read and deepCAGE (Cap Analysi

82 the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, US

83 epetitive sequences prevents pre-assembly of long reads in the relevant genomic region.

84 e evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans ge

85 , such as BAC clone end sequences and PacBio long reads, indicate misassembled regions.

86 n with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at

87 de-novo assembly for metagenomes using only long reads is gaining attention.

88 Using Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq), we developed an

89 acific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline ca

90 rinciples: (i) Compact representation of the long reads leads to efficient alignments.

91 The long read length enables PacBio sequencing to close gaps

92 Here, we use long read length ultra-deep resequencing-by-synthesis to

93 n length and their analysis does not require long read length.

94 zed single DNA polymerases in ZMW arrays for long-read-length DNA sequencing.

95 ng packages were incapable of assembling the long read lengths (5-50 kbp) at such high error rates (b

96 This method is amenable to long read lengths and will likely enable mapping of meth

97 Speed, single-base sensitivity and long read lengths make nanopores a promising technology

98 it is not vulnerable to GC bias, it produces long read lengths, and its kinetic information is sensit

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

100 Nanopore sequencing promises long read-lengths and single-molecule resolution, but th

101 Sequences need to be either long reads (longer than 100 bp) or joined paired-end rea

102 a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample

103 nION sequencing data sets against short- and long-read mappers indicates that GraphMap increases mapp

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

105 ng high-throughput short-read platforms with long-read mapping.

106 the only new technology ready to produce the long reads most suitable for the de novo sequencing and

107 to derive the compact representation of the long reads, motivating an algorithmic conversion from a

108 g technology (PacBio SMRT) that produces the long reads necessary to discriminate the complexity of H

109 We hypothesize that these ultrafast long reads on chips can be achieved because the combined

110 roaches that exploit the high mappability of long reads, PBHoney is demonstrated as being effective a

111 nships among the short reads governed by the long read process via a Markov Random Field.

112 ngth read sets, including capillary reads or long reads promised by the third generation sequencing t

113 ied version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read

114 nome assembly) for P. dactylifera, using the long-read pyrosequencing platform (Roche/454 GS FLX Tita

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

116 elatively low identity requirement so that a long read region can be aligned to at least one contig r

117 ch makes it possible to further refine these long read regions with the initial insufficient short re

118 Even though some long read regions without the true genome regions in the

119 ed by a high error rate, and assembling from long reads require a high depth of coverage.

120 ination of single read, paired-end read, and long read RNA sequencing.

121 Technologies such as Synthetic long-read RNA sequencing (SLR-RNA-seq) delivered 5 milli

122 ntroduce an RNA sequencing method, synthetic long-read RNA sequencing (SLR-RNA-seq), in which small p

123 RACE (rapid amplification of cDNA ends) and long-read RNA sequencing.

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

125 For long read sequence mapping, there are limited options; B

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

127 MinION long-read sequence data also facilitated the elucidation

128 ombined without barcoding and simultaneously long-read sequenced using a single SMRT cell.

129 be avoided if the opportunities provided by long-read sequencers are to be fully exploited.

130 The long-read sequencers from Pacific Bioscience (PacBio) an

131 bly algorithms and the recent development of long-read sequencers, split mapping will soon be the pre

132 iation data on the 1000 Genomes samples from long read sequencing and other technologies, and will co

133 Taken together, our data indicate that such long read sequencing data can be used to affordably sequ

134 tractable, thanks to the development of new long read sequencing technologies.

135 ecautions must also be undertaken when using long read sequencing technology, which may also lead to

136 The recent developments in long reads sequencing methods offer a promising way to a

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

138 Long-read sequencing can overcome the weaknesses of shor

139 LCON and FALCON-Unzip algorithms to assemble long-read sequencing data into highly accurate, contiguo

140 reads can be derived from, for example, raw long-read sequencing data or contigs and scaffolds comin

141 bp with respect to the human reference, with long-read sequencing data providing a fivefold increase

142 results indicate that haploid resolution of long-read sequencing data will significantly increase se

143 d a pipeline for transcript annotation using long-read sequencing data.

144 nt study demonstrates the general utility of long-read sequencing for the time-course analysis of glo

145 ly, derived from a combination of short- and long-read sequencing in conjunction with optical mapping

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

147 Using single-molecule long-read sequencing of 16 diverse fungal genomes, we ob

148 Here we use unbiased long-read sequencing of full-length neurexin (Nrxn)1alph

149 Furthermore, long-read sequencing of the transcriptome reveals novel

150 In addition, the use of SMRT long-read sequencing offered the ability to examine alte

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

152 the promoter) as functionally consequential, long-read sequencing revealed that this signal was drive

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

154 Long-read sequencing technologies have the potential to

155 Long-read sequencing technologies provide high-resolutio

156 Long-read sequencing technologies such as Pacific Biosci

157 In the context of third-generation long-read sequencing technologies, read-overlap-based ap

158 read length making it better suited for new long-read sequencing technologies.

159 a versatile new sample preparation tool for long-read sequencing technologies.

160 pting to phase variants using amplicon-based long-read sequencing technologies.

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

162 Here we use single-molecule long-read sequencing technology from Pacific Biosciences

163 to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to

164 Hall et al. have strategically used long-read sequencing technology to characterize the stru

165 Incorporation of synthetic long-read sequencing technology with standard short-read

166 ently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual l

167 advantage of the contiguity associated with long-read sequencing to generate a high-quality assembly

168 Here we use long-read sequencing to generate end-to-end genome assem

169 e, we used single-molecule amplification and long-read sequencing to study the HIV-1 provirus, which

170 dual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoCh

171 ciation in the same molecule, requires deep, long-read sequencing.

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

173 transcription polymerase chain reaction and long-read sequencing.

174 ts a powerful alternative to single-molecule long-read sequencing.

175 ur experiments on metagenomes assembled from long reads show that BIGMAC can improve assembly quality

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

177 e time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing a

178 In this study, we used long-read single molecule, real-time (SMRT) sequencing t

179 ere, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequenc

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

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

182 Long-read single-molecule sequencing has revolutionized

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

184 Long-read, single-molecule real-time (SMRT) sequencing i

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

186 New synthetic long read (SLR) technologies promise significant advance

187 LoRMap, a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequenci

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

189 ccurate, requiring researchers to use older, long-read technologies.

190 subsequent assembly (e.g. when one is using 'long read' technologies like those offered by PacBio or

191 r to those obtained using the more expensive long-read technology.

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

193 in projects with relatively low coverage by long reads) thus reducing the overall cost of genome seq

194 HALC aligns the long reads to short read contigs from the same species w

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

196 The recently introduced TruSeq synthetic long read (TSLR) technology generates long and accurate

197 st reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequenc

198 gnment Process (MHAP) for overlapping noisy, long reads using probabilistic, locality-sensitive hashi

199 With 6.8x mapped coverage of mangabey PacBio long-reads we addressed 97% of gaps and closed 66% of ad

200 With 4x mapped coverage of PacBio long-reads we saw reads address 63% of gaps in our budge

201 , by combining Illumina short-read data with long reads, we phased both single-nucleotide variants an

202 With 24x mapped coverage of PacBio long-reads, we addressed 99% of gaps and were able to cl

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

204 gration of Third Generation Sequencing (TGS) long reads with Second Generation Sequencing (SGS) short

205 or rates and a fast graph traversal to align long reads with speed and high precision (>95%).

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

207 Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a pot