ライフサイエンスコーパス: assembler

1 operation of the "compartmentalized shotgun assembler".

2 bler based on these called SGA (String Graph Assembler).

3 f nucleotide sequence assembly programs (DNA assemblers).

4 y; and AMOScmp, the first comparative genome assembler.

5 ead of complete genes, may be reported by an assembler.

6 e and assembled with DNAStar's SeqMan genome assembler.

7 s use the TGICL tool, Megablast and the CAP3 assembler.

8 y assembled de novo by the CLC Assembly Cell assembler.

9 assemblies, but were reduced using the SKESA assembler.

10 econstruct genes that were fragmented by the assembler.

11 p-LR, a reference-based long-read transcript assembler.

12 el is twice that of a standard transcriptome assembler.

13 wtie2 mapping program and the SPAdes genomic assembler.

14 ly compared with the performance of the base assembler.

15 v3 license from sourceforge.net/projects/spa-assembler.

16 nst high sequencing error rate than the base assembler.

17 ng time of existing overlap-layout-consensus assemblers.

18 tion, affecting the relative ranking of some assemblers.

19 prove the contigs and scaffolds from several assemblers.

20 d data and assumptions and heuristics of the assemblers.

21 with assembly using off-the-shelf long-read assemblers.

22 species may behave like repeats and confuse assemblers.

23 d contiguity than state-of-the-art long-read assemblers.

24 rehensive studies on the evaluation of these assemblers.

25 e accuracy of assembly obtained by different assemblers.

26 consistently outperforming other metagenome assemblers.

27 methods, alongside 4 upstream aligners and 7 assemblers.

28 M and increase the scalability of metagenome assemblers.

29 ignificant outperformance over existing meta-assemblers.

30 s existing meta-assemblers and single-sample assemblers.

31 haplotype-specific contigs compared to other assemblers.

32 ich is a core algorithm at the heart of most assemblers.

33 he assembly, we propose SAUTE and SAUTE_PROT assemblers.

34 theory but also in the output of widely used assemblers.

35 y compared to the other available mitogenome assemblers.

36 ifficult even for state-of-the-art long-read assemblers.

37 d to the state-of-the-art viral quasispecies assemblers.

38 embly quality metric) compared with existing assemblers.

39 k -mer occurs, which is key in transcriptome assemblers.

40 t-resolution capabilities of de Bruijn graph assemblers.

41 cused on pre-processing reads and optimizing assemblers.

42 requires less memory space than most of the assemblers.

43 re the performance of EPGA and other popular assemblers.

44 that IVA outperforms all other virus de novo assemblers.

45 of magnitude on large genomes versus Celera Assembler 8.2.

46 In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for

47 In this paper we introduce ITD Assembler, a novel approach that rapidly evaluates all u

48 ll our system the Maryland Super-Read Celera Assembler (abbreviated MaSuRCA and pronounced 'mazurka')

49 Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly

50 all, medium, and large genomes shows that JR-Assembler achieves a better or comparable overall assemb

51 Finally, a simulation study shows that JR-Assembler achieves a superior performance on memory use

52 The recently developed plasmidSPAdes assembler addressed some of these challenges in the case

53 Transcriptome assemblers aim to reconstruct full-length transcripts fr

54 higher precision in average compared to meta-assemblers Aletsch, TransMeta, and PsiCLASS, respectivel

55 t consensus regardless of sequence platform, assembler algorithm, or coverage.

56 mory required by traditional de Bruijn graph assemblers, allowing millions of reads to be assembled v

57 s (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to th

58 ly graphs provided by a conventional de novo assembler and alignments of paired-end reads to assemble

59 he manual pipeline of NCTC based on the HGAP assembler and Circlator.

60 aHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similari

61 es against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quali

62 n assembly varies enormously among different assemblers and different genomes; and third, that the co

63 sted reference-based assembly using multiple assemblers and modes; gene predictor combining; and func

64 er 2 outperforms other de novo transcriptome assemblers and offers accurate and efficient analysis of

65 produce multiple assemblies using different assemblers and parameters, then select the best one for

66 Sophisticated computer algorithms (assemblers and scaffolders) merge these DNA fragments in

67 nal genomics applications, including de novo assemblers and sequence matching programs for SNP callin

68 ncorporated into chimeric contigs across all assemblers and sequencing technologies, while more abund

69 benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparab

70 aver substantially outperforms existing meta-assemblers and single-sample assemblers.

71 ssemblies from the GAGE study to rank genome assemblers and to compare EvalDNA to two other quality e

72 Multidomain peptides are one such assembler, and in previous work we have demonstrated the

73 mbly, we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish a

74 ree different assembly programs (PHRAP, TIGR Assembler, and STROLL) on the DNA fragments used in both

75 Tools and pipelines like the assembler, and the workflow management environments make

76 rrected reads are assembled using the Celera Assembler; and (iii) the assembly is polished using a pr

77 We determined that a multi-assembler approach improves eukaryotic metatranscriptome

78 , and the other is the "whole genome shotgun assembler" approach, favored by researchers at Celera Ge

79 incorporation of this method into the Celera Assembler are reported for the D. melanogaster, H. sapie

80 Although most existing genome assemblers are based on de Bruijn graphs, the constructi

81 ications is being expanded, the existing SLR assemblers are optimized for a narrow range of parameter

82 As a rule, modern assemblers are usually designed to assemble genomes with

83 (Phred, a base-caller, and Phrap, a sequence assembler) are applied to assess the quality of each bas

84 elles and force generators (motors and track assemblers) are linked, forming an organelle-based, cell

85 theoretically predict the existence of these assembler artifacts and confirm and measure the extent o

86 be the relative performance of the different assemblers as well as other significant differences in a

87 h allows to bypass the limitations of modern assemblers associated with a huge amount of data being p

88 Current genomic sequence assemblers assume that the input data is derived from a

89 Moreover, most assemblers assume uniform read coverage, condition that

90 he most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy.

91 iCLASS, an accurate and efficient transcript assembler based on an approach that simultaneously analy

92 pressed Burrows-Wheeler transform, and a new assembler based on these called SGA (String Graph Assemb

93 sible groups, is a key element of the entire assembler, because it permits a simple approach to paral

94 In this study, we present a novel de novo assembler, BinPacker, by modeling the transcriptome asse

95 his paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic dataset

96 We also show that most published paired read assemblers calculate incorrect posterior quality scores.

97 used to build a next-generation whole genome assembler called BOA (Berkeley Open Assembler) that will

98 We developed a new de novo assembler called IVA (Iterative Virus Assembler) designe

99 requirements, we propose an extension-based assembler, called JR-Assembler, where J and R stand for

100 trate how the modular nature of this peptide assembler can be designed for biological applications.

101 We show that DNA assembler can rapidly assemble a functional D-xylose uti

102 Long-read metagenome assemblers can generate contiguous bacterial chromosomes

103 Although modern long-read assemblers can often assemble these genes, using existin

104 While various NGS assemblers can use information from several libraries of

105 Most assemblers cannot handle the amount of input sequence da

106 show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencin

107 re implementation, Cortex, the first de novo assembler capable of assembling multiple eukaryotic geno

108 Thus, building a trio-aware assembler capable of producing accurate and chromosomal-

109 ncing technologies, making it one of the few assemblers capable of handling such mixtures.

110 Phylogenetic clustering showed that all assemblers captured a proportion of the most divergent l

111 Resource-efficient genome assemblers combine both the power of advanced computing

112 oid locus as produced by the original Celera Assembler consensus algorithm.

113 e Integrated Network and Dynamical Reasoning Assembler consisting of millions of text-triple pairs ex

114 ions of high heterozygosity often results in assemblers creating two copies rather than one copy of a

115 e present HiCanu, a modification of the Canu assembler designed to leverage the full potential of HiF

116 gest datasets using MetaHipMer, a metagenome assembler designed to run on supercomputers and large cl

117 e novo assembler called IVA (Iterative Virus Assembler) designed specifically for read pairs sequence

118 We present TransComb, a genome-guided assembler developed based on a junction graph, weighted

119 Current metagenome assemblers developed for short sequence reads or noisy l

120 er can be considered as a gap-based sequence assembler, different gap sizes result in an almost const

121 In addition, different assemblers displayed distinct memory/speed trade-offs in

122 euler, in contrast to the celera assembler, does not mask such repeats but uses them inst

123 Integrating MHAP with the Celera Assembler enabled reference-grade de novo assemblies of

124 ; rather, having a fast, scalable metagenome assembler enables a user to more easily perform coassemb

125 competitive than the other compared de novo assemblers especially with precision measure, due to the

126 and achieves much higher accuracy than other assemblers, especially for alternatively spliced genes a

127 named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenov

128 However, in contrast to the Celera assembler, EULER-DB does not mask repeats but uses them

129 r exceeded the best performing genome-guided assemblers even when the transcriptomes included isoform

130 into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of

131 Most existing assemblers failed to generate high-quality phased assemb

132 text of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads in

133 s step also allows the use of any standalone assembler for generating the final scaffolds.

134 We present Aletsch, a new assembler for multiple bulk or single-cell RNA-seq sampl

135 We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads.

136 ce a novel tool that employs a syncmer-based assembler for rapid assembly graph construction, integra

137 We developed coronaSPAdes, a novel assembler for RNA viral species recovery in general and

138 and memory requirements of the Velvet/Oasis assembler for the datasets used in this study by 60-85%

139 rch community to choose the most appropriate assembler for their data and identify possible improveme

140 MaSuRCA against two of the most widely used assemblers for Illumina data, Allpaths-LG and SOAPdenovo

141 The development of dedicated assemblers for metagenomic data was a relatively late in

142 es are required to evaluate the various read assemblers for metagenomic studies.

143 Few de novo assemblers for transposable elements exist, and most hav

144 r method is also flexible to embed different assemblers for various types of target genomes.

145 Traditional single-sample assemblers frequently produce fragmented transcripts, es

146 olated and assembled using the SPAdes hybrid assembler from the Illumina short-read and PacBio long-r

147 he aforementioned problems prohibit existing assemblers from getting satisfactory assembly results.

148 The output of a genome assembler generally comprises a collection of contiguous

149 ers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and h

150 Among women, only machine assemblers had significantly increased ALS mortality (ra

151 us benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) asse

152 The Phusion assembler has assembled the mouse genome from the whole-

153 and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better

154 cently a number of de novo and mapping-based assemblers have been developed to produce high quality d

155 HiFi data, the genome was assembled with two assemblers, HiCanu and Hifiasm, followed by scaffolding

156 ironmental metagenomes using seven prominent assemblers (IDBA-UD, MEGAHIT, Canu, Flye, Opera-MS, meta

157 ITD Assembler identified the highest percentage of reported

158 nomes generated by a wide variety of de novo assemblers if a good reference assembly of a closely rel

159 produced by deep sequencing, such as de-novo assemblers, ignore the underlying diversity.

160 n particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of B

161 Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular

162 that it improves on the state-of-the-art SLR assemblers in accuracy and speed.

163 showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accurac

164 has been considerable debate about molecular assemblers in the context of nanotechnology, our demonst

165 ther popular short-read metagenome and viral assemblers in the recovery of full-length RNA viral geno

166 Most recent assemblers include a scaffolding module; however, users

167 ts in both recall and precision over leading assemblers, including StringTie, Cufflinks, Bayesembler,

168 ient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using compa

169 cells: iron transporter, iron-sulfur cluster assembler, iron-storage protein, antioxidant and stimula

170 The molecular assembler is a supramolecular aggregate of bifunctional

171 ITD Assembler is a very sensitive tool which can detect part

172 Multicomponent Assembler is expected to be a unique cyberinfrastructure

173 The critical stage of every de novo genome assembler is identifying paths in assembly graphs that c

174 Microarray Data Assembler is specifically designed to simplify this task

175 t: first, that data quality, rather than the assembler itself, has a dramatic effect on the quality o

176 The Verkko assembler later automated this process, achieving comple

177 Available de novo assemblers leave repetitive portions of the genome poorl

178 of long, HiFi reads, we present the La Jolla Assembler (LJA), a fast algorithm using the Bloom filter

179 The choice of reference assembler, mapper and variant caller also significantly

180 Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genom

181 technology, our demonstration that primitive assemblers may arise from simple phase separated reactan

182 nd laboratory technicians and female machine assemblers may be at increased risk of death from ALS, s

183 We developed MULTIDOMAIN ASSEMBLER (MDA) to address the special problems that ari

184 We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for

185 and memory usage of three popular metagenome assemblers (MetaSPAdes, MEGAHIT, and MetaHipMer2) in dat

186 The fast but less accurate assembler Miniasm can be used for quick initial assembly

187 present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembli

188 e of repeat analyses, the Assisted Automated Assembler of Repeat Families algorithm has been develope

189 levels of Survival of Motor Neuron, a master assembler of spliceosomal components.

190 best-characterized function of SMN is as an assembler of spliceosomal small nuclear ribonucleoprotei

191 This complex acts as an "assembler" of [4Fe-4S] clusters; i.e., the two GRX5-dona

192 he SMN complex is the identifier, as well as assembler, of the abundant class of snRNAs in cells beca

193 xisting genome, metagenome and transcriptome assemblers often are not able to assemble many viruses (

194 We tested ITD Assembler on The Cancer Genome Atlas AML dataset as a tr

195 evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes

196 outperforms almost all the existing de novo assemblers on all the tested datasets, and even outperfo

197 pared them with the state-of-the-art de novo assemblers on both simulated and real datasets.

198 ehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes

199 ecifically compared the performance of these assemblers on low-abundance species, which include clini

200 We found that PMem can enable metagenome assemblers on terabyte-sized datasets by partially or fu

201 curacy of the EC components of existing HiFi assemblers on the CHM13 and the HG002 datasets and furth

202 tasets, and even outperforms those ab initio assemblers on the real dog dataset.

203 en molecular rotor and a synthetic molecular assembler or pump, are discussed.

204 imited by the constraints of bulk sequencing assemblers or pre-sorting throughput.

205 Compared to state-of-the-art assemblers, our algorithm not only achieves five-fold fe

206 le for base-accurate gene identification, SR assemblers outperform other options.

207 longer, indicating that the advantages of JR-Assembler over current assemblers will increase as the r

208 Finally, the SPAdes assembler performed the best.

209 ribe a targeted approach with a novel genome assembler PhaseDancer that extends SD-rich regions of in

210 mpled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted gene

211 compare unigene sets generated by different assemblers: Phrap, Cap3 and Cap4.

212 ine the first complete structures of the key assembler protein, SMN, and the truncated isoform, SMNDe

213 e WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the

214 For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even

215 However, most de novo assemblers require enormous amount of computational reso

216 Existing long-read assemblers require thousands of central processing unit

217 onnect contigs into larger scaffolds or help assemblers resolve ambiguities in repetitive regions of

218 with similar improvements over single-sample assemblers Scallop2 (10.1%-43.6%) and StringTie2 (24.3%-

219 arameter selection and execution of multiple assemblers, scores the resulting assemblies based on mul

220 Most assemblers select a single assembly according to ad hoc

221 compare assembly quality across a variety of assemblers, sequence data types, and parameter choices.

222 Using MHAP and the Celera Assembler, single-molecule sequencing can produce de nov

223 Our proposed meta-assembler Slicembler partitions the input data into opti

224 In comparison with three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD and MetaVelvet), Omega p

225 framework is based on a novel short peptide assembler (SPA) that assembles protein sequences from th

226 etagenome." A recently developed single-cell assembler, SPAdes, in combination with contig binning me

227 mbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repeti

228 de novo short-read genome and transcriptome assemblers start by building a representation of the de

229 The use of five different assemblers starting from subsampled data allowed us to e

230 once it reaches a critical concentration the assembler starts to produce polymers instead of supramol

231 over the past three decades, modern de novo assemblers still struggle to accurately reconstruct high

232 ansfer method TOGA, BRAKER3, and the RNA-seq assembler StringTie were consistently top performers acr

233 Popular de Bruijn graph assemblers, such as IDBA-UD, generate high-quality assem

234 red to as Scoring-and-Unfolding Trimmed Tree Assembler (SUTTA), and present experimental results on s

235 Existing WGS assemblers take a column-by-column approach to consensus

236 R-DB algorithm that, similarly to the Celera assembler takes advantage of clone-end sequencing by usi

237 e present a new transposable element de novo assembler, Tedna, which assembles a set of transposable

238 , it generated the longest contigs among all assemblers tested.

239 ercome this challenge, we present an RNA-seq assembler that allows the determination of the expressed

240 We present a new Eulerian assembler that generates nearly optimal short read assem

241 llop, an accurate reference-based transcript assembler that improves reconstruction of multi-exon and

242 hese issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single

243 scovery of a rudimentary synthetic molecular assembler that produces polymers.

244 We present HINGE, an assembler that seeks to achieve optimal repeat resolutio

245 Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity seq

246 StringTie2, a reference-guided transcriptome assembler that works with both short and long reads.

247 recent development is the implementation of assemblers that are built according to explicit statisti

248 Most state-of-the-art assemblers that can achieve relatively high assembly qua

249 Those assemblers that do report uncertainty take different app

250 Unlike other graph-based assemblers that only aim to maintain the contiguity of o

251 graph model of assembly, unlike most de novo assemblers that rely on de Bruijn graphs, and is simply

252 nly known viable path to utilize NGS de novo assemblers that require more memory than that is present

253 e genome assembler called BOA (Berkeley Open Assembler) that will easily scale to mammalian genomes.

254 The state-of-the-art sequence assemblers then construct the whole genomic sequence fro

255 developed a targeted iterative graph routing assembler, TIGRA, which implements a set of novel data a

256 c design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel compu

257 quence assembly was produced using the Atlas assembler to combine whole genome shotgun sequences with

258 l, available at that can be combined with an assembler to generate an assembly without intron retenti

259 munication, SGA provides the first practical assembler to our knowledge for a mammalian-sized genome

260 HDMBr also acted like a molecular assembler to promote the assembly of chondroitin sulfate

261 We introduce a two-stage assembler to utilize the full length of nanopore reads.

262 Meanwhile, BLESS can extend reads like DNA assemblers to correct errors at the end of reads.

263 It is nearly impossible for these DNA assemblers to handle the huge amount of data produced by

264 Hifieval will help HiFi assemblers to improve EC and assembly quality in the lon

265 ariants and contamination set a high bar for assemblers to process viral datasets with diverse proper

266 ved quality of the resulting sequences allow assemblers to produce longer contigs while using less me

267 In contrast, using the popular assembler tool Trinity (r2013-02-25), only 14 transcript

268 by precision), Aletsch surpasses the leading assemblers TransMeta by 22.9%-62.1% and PsiCLASS by 23.0

269 Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcript

270 Without special modifications, assemblers tuned for homogeneous sequence data may perfo

271 Each assembler type's strengths were maintained even when our

272 Both assemblers use de Bruijn graph on reads.

273 and methods are freely available, as are all assemblers used in this study.

274 see text] compared to the resource-efficient assemblers using benchmark datasets from GAGE and Assemb

275 sive comparison of JR-Assembler with current assemblers using datasets from small, medium, and large

276 However, many DNA assemblers using overlap graphs suffer from the need for

277 We compare our software to current assemblers using simulated and real data.

278 Many de novo assemblers using the de Bruijn graph of a set of the RNA

279 assembly method, referred to as Viral Genome Assembler (VGA).

280 embly optimization pipeline based on Trinity assembler was developed to obtain a reference Hydration-

281 Celera Assembler was modified for combinations of ABI 3730 and

282 The performance of different assemblers was compared in terms of phylogenetic cluster

283 Omega (overlap-graph metagenome assembler) was developed for assembling and scaffolding

284 bly results from multiple long-read data and assemblers, we demonstrate that in addition to providing

285 The 11 assemblers were evaluated using quality assessment tool

286 ntral processing unit time than most current assemblers when the read length is 150 bp or longer, ind

287 pose an extension-based assembler, called JR-Assembler, where J and R stand for "jumping" extension a

288 troduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of partic

289 Here, we report a new method, DNA assembler, which allows the assembly of an entire bioche

290 g error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OL

291 mplemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/

292 hen assembles the mega-reads using the CABOG assembler, which was designed for long reads.

293 ment of a new generation of de novo sequence assemblers, which all have sequencing error correction (

294 We propose that Scy is a molecular "assembler," which, by sequestering DivIVA, promotes the

295 the advantages of JR-Assembler over current assemblers will increase as the read length increases wi

296 An extensive comparison of JR-Assembler with current assemblers using datasets from sm

297 The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homo

298 de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approac

299 posite conclusions can arise when evaluating assemblers with different annotations.

300 mbines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bru