ライフサイエンスコーパス: genome assembly

1 hich extracts paths from De Bruijn graph for genome assembly.

2 regions are missing from the current chicken genome assembly.

3 g has become a state-of-the-art technique in genome assembly.

4 candidates which increase the difficulty of genome assembly.

5 gions were detected and corrected in the new genome assembly.

6 omosomes is an essential step during de novo genome assembly.

7 l these changes in EPGA2 are more useful for genome assembly.

8 ong been thought to be recalcitrant to whole-genome assembly.

9 olyploid and heterozygous, which complicates genome assembly.

10 is important to establish best practices for genome assembly.

11 ordinates, LRGs include mapping to the human genome assembly.

12 to LGs, accounting for over 97% of the total genome assembly.

13 ded that there is no single best approach to genome assembly.

14 orm assembly, haplotype phasing, and de novo genome assembly.

15 ere sequences available in the current human genome assembly.

16 llected during mutant mapping to improve the genome assembly.

17 e yet not annotated in the most recent human genome assembly.

18 n of rapid microbial identification and full-genome assembly.

19 ntial to address limitations associated with genome assembly.

20 caffold anchoring data to improve the potato genome assembly.

21 he development of numerous novel methods for genome assembly.

22 AP predicts protein-coding genes in a fungal genome assembly.

23 xpertise on methodologies and techniques for genome assembly.

24 the alternative de Bruijn graph approach to genome assembly.

25 f an assembly, and tracks changes to updated genome assemblies.

26 what governs completeness and contiguity of genome assemblies.

27 thin a species that is not present in static genome assemblies.

28 rotypes), from both raw sequencing reads and genome assemblies.

29 PS is a useful tool in building high-quality genome assemblies.

30 ins one of the major challenges of finishing genome assemblies.

31 aid others looking to improve existing draft genome assemblies.

32 eq) to facilitate the scaffolding of de novo genome assemblies.

33 where it is easy to produce very fragmentary genome assemblies.

34 for ultra-long-range scaffolding of de novo genome assemblies.

35 orthologous proteins to improve low quality genome assemblies.

36 sharp increase in the number of species with genome assemblies.

37 lizing synteny between two or more annotated genome assemblies.

38 ainst a vast collection of quality reference genome assemblies.

39 of dramatically improving the contiguity of genome assemblies.

40 hensive validation and refinement of de novo genome assemblies.

41 Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequen

42 mparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides

43 New data highlights include seven new genome assemblies, a Neandertal genome data portal, phen

44 s a foundational resource in comparative and genome assembly activities.

45 As a result of improvements in genome assembly algorithms and the ever decreasing costs

46 ecting and analyzing variants from a de novo genome assembly aligned to a reference genome.

47 and other annotation tracks, the additional genome assemblies and an embedded VISTA genome compariso

48 Our genome assemblies and annotations also provide comprehen

49 grow, providing a comprehensive resource of genome assemblies and annotations to scientists and stud

50 o implement complicated pipelines to produce genome assemblies and annotations very quickly.

51 a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resourc

52 mportantly, extension of the newly corrected genome assemblies and gene models to 15 other newly asse

53 mapping can be used as a validation tool for genome assemblies and how to interpret the results.

54 eased availability of high-quality reference genome assemblies and methods to profile single-base res

55 ing IWGSC CSSv2 and TGACv1 Triticum aestivum genome assemblies and reassembling or mapping of IWGSC C

56 These sequences are largely missing from the genome assemblies and represent the youngest and most ho

57 alyzing information from a large database of genome assemblies and their associated annotations.

58 To guarantee clean genome assemblies and to prevent the introduction of con

59 osomal DNA (rDNA) is not included in current genome assemblies and, consequently, genomic analyses to

60 Using a draft Oxytricha genome assembly and a custom-written protein-coding gene

61 propose an open-source library dedicated to genome assembly and analysis to fasten the process of de

62 ver 189 tools, including population genetic, genome assembly and analysis tools, as well as metagenom

63 To date, there have been only two genome assembly and annotation efforts with neither asse

64 Complete and accurate genome assembly and annotation is a crucial foundation f

65 The M. sympodialis genome assembly and annotation presented here is at a qu

66 s, and maintains and updates the A. thaliana genome assembly and annotation.

67 imate completeness during different steps of genome assembly and annotation.

68 ing has sparked a new wave of development of genome assembly and assembly validation methods.

69 scribe a high-quality domestic cat reference genome assembly and comparative inferences made with oth

70 Genome assembly and comparison of read coverage in male

71 l purpose: delivering a contiguous, complete genome assembly and creating a full catalog of correctly

72 tRF-license plate') that is independent of a genome assembly and does not require any brokering mecha

73 lecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction

74 e describe an approach to performing de novo genome assembly and experimental phasing by integrating

75 embryonic development, based on an improved genome assembly and gene model set, refined functional g

76 test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression da

77 V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce geno

78 ture allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny an

79 heir repetitive nature poses a challenge for genome assembly and makes progress on the detailed study

80 Subassembly may facilitate accurate de novo genome assembly and metagenome sequencing.

81 Advances in genome assembly and phasing provide an opportunity to in

82 of-of-concept utility with respect to hybrid genome assembly and polymorphism detection.

83 rate assembly generated thus far using whole-genome assembly and scaffolding methods.

84 y NGS platforms necessitate quality control, genome assembly and sequence similarity searching before

85 Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five S

86 hat the performance of tasks such as de novo genome assembly and SNP calling can be dramatically impr

87 The genome assembly and these associated analyses provide cr

88 ermore, Clinical PathoScope does not rely on genome assembly and thus can more rapidly complete the a

89 oject, different completeness scores for the genome assembly and/or gene space should be determined.

90 alignments, comparative analyses of multiple genome assemblies, and consistency with optical and othe

91 fered additional support for our local tumor genome assemblies, and identified the birth of a novel e

92 rial genome with a comprehensive single-cell genome assembly, and make over 800 changes (insertions,

93 r systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative geno

94 rence strain shows that incomplete reference genome assemblies are a major source of noise.

95 mes where chromosomes are incomplete and sub-genome assemblies are collapsed.

96 suggesting that comparisons among additional genome assemblies are not likely to result in the discov

97 Draft de novo genome assemblies are now available for many organisms.

98 Reference genome assemblies are subject to change and refinement f

99 ojects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome

100 of the best ways to detect errors in de novo genome assemblies, as well as to orient and place assemb

101 In genome assembly, as coverage of sequencing and genome si

102 We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole

103 b in length, which have enabled high-quality genome assembly at an affordable cost.

104 sample tracking and a tool for managing the genome assemblies available to perform an analysis.

105 genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1).

106 e potential to produce gold-standard de novo genome assemblies, but fully exploiting error-prone read

107 nstrate AlignGraph's efficiency in improving genome assemblies by taking advantage of closely related

108 y annotated on the human and mouse reference genome assemblies by the National Center for Biotechnolo

109 al maps resulted in a chromosome-level draft genome assembly comprising 193 Mbp, or 53% of the 367 Mb

110 to help the user identify which contigs in a genome assembly contain gene targets and to optimize ana

111 hat short sequence reads can be aligned to a genome assembly containing a single rDNA repeat.

112 The largest gaps in the human genome assembly correspond to multi-megabase heterochrom

113 es stable accessioning and data tracking for genome assembly data.

114 for diverse applications, including de novo genome assembly, deconvolution of metagenomic samples an

115 ethods for using optical map data to enhance genome assemblies derived from both traditional sequence

116 Genome assembly efforts and future builds of the human g

117 velop an algorithm, called extract paths for genome assembly (EPGA), which extracts paths from De Bru

118 For reducing peak memory in genome assembly, EPGA2 adopts memory-efficient DSK to co

119 Downstream studies such as genome assembly, epidemiologic screening, and a culture

120 l subproblem in many applications, including genome assembly, error correction of sequencing reads, f

121 Further, the MinION-derived genome assembly expanded the C. elegans reference genome

122 que and Malayan flying lemur); eight updated genome assemblies; extended support for new data types s

123 As input, BRAKER1 requires a genome assembly file and a file in bam-format with splic

124 fically, CPT-seq data is mapped to a de novo genome assembly, followed by the identification of pairs

125 long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subp

126 puzzles, by generation and analysis of whole genome assemblies for 16 Anopheles species, with genomic

127 With the ubiquitous generation of complete genome assemblies for a variety of species, efficient to

128 ies were used to generate de novo and hybrid genome assemblies for four different bacteria, which wer

129 Our approach enables acquisition of genome assemblies for individual uncultivated bacteria u

130 Whole-genome assemblies for the great apes provide remarkable

131 n addition, we have also generated two draft genome assemblies for the red and green varieties.

132 Here we report near complete genome assemblies for three Pneumocystis species that in

133 ive and experimental analysis of a reference genome assembly for a double haploid YY male garden aspa

134 Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contras

135 Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and s

136 Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.).

137 In this study, we generated a genome assembly for C. roseus that provides a near-compr

138 Here we provide a high-quality genome assembly for cassava with improved contiguity, li

139 We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, iden

140 assembly and introduce a second white spruce genome assembly for genotype WS77111.

141 -read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), compris

142 enome assembly, which had been the reference genome assembly for over 7 years.

143 We demonstrate efficient genome assembly for several microorganisms using as few

144 The availability of a high-quality genome assembly for the elite maize inbred PH207 expands

145 Here, we report on a high-quality genome assembly for the K. marmoratus South Korea (SK) s

146 antage of the availability of a high-quality genome assembly for the little brown bat, Myotis lucifug

147 Here we develop a high-quality reference genome assembly for threespine sticklebacks.

148 approach that will lead to a reference-grade genome assembly for Upland cotton.

149 ressed sequence tags or ESTs and mapped to a genome assembly) for P. dactylifera, using the long-read

150 ence and annotations for current versions of genome assemblies from the NCBI genomes FTP site.

151 sted the efficacy of SCG to generate a draft genome assembly from a single sample, in this case a cel

152 tomating all steps in the process of de novo genome assembly from Illumina data.

153 An accurate genome assembly from short read sequencing data is criti

154 Stylophora pistillata, combined with a draft genome assembly from the cnidarian host cells of the sam

155 rated a high-quality transcriptome and draft genome assembly from the first bacteria-free P. chromato

156 metazoans Capsaspora owczarzaki, and a draft genome assembly from the homoscleromorph sponge Oscarell

157 any other host species and demonstrate viral genome assembly from viral piRNAs in the absence of vira

158 y decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the a

159 ting and understanding the complexities of a genome assembly, from the overall genome structure down

160 genomic regions are missing from the current genome assembly (Galgal5), which should be resolved in f

161 ng most of these regions unresolved in newer genome assemblies generated primarily by next-generation

162 le alignments of genomic sequences and whole-genome assemblies, has become one of the standard techni

163 Thus, to date, about 1800 bacterial genome assemblies have been "finished" at great expense

164 In the past year 19 new genome assemblies have been added, and we anticipate rel

165 the year of 2014 more than 10,000 microbial genome assemblies have been publicly released bringing t

166 Genome assemblies have been published for various primat

167 ags per sample and mapped to reference human genome assembly hg19.

168 This study i) provided a 10 Mb targeted genome assembly; ii) demonstrated NGS of BAC pools as a

169 luable new tool for improving the quality of genome assemblies in complex DNA regions.

170 short-read assembly methods to create draft genome assemblies in just days.

171 bout the molecular driving forces underlying genome assembly in an intracellular environment and its

172 scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely relate

173 approach to deal with the problem of de novo genome assembly in the presence of ultra-deep sequencing

174 The genome assembly includes nuclear (~29 Mb) and organellar

175 aluation of results using simulated and real genome assemblies indicates that our approach can substa

176 describe our rapidly developing services for genome assembly information and outline further major de

177 ified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein

178 The genome assembly is comprised of nearly 14,000 intron-con

179 late genes over long distances, a contiguous genome assembly is crucial for predicting and understand

180 Genome assembly is difficult due to repeated sequences w

181 Accurate and contiguous genome assembly is key to a comprehensive understanding

182 Although annotating a eukaryotic genome assembly is now within the reach of non-experts,

183 The results show that nearly 5% of the genome assembly is occupied by ERV-derived sequences, a

184 De novo genome assembly is one of the most important steps to re

185 A crucial problem in genome assembly is the discovery and correction of misas

186 ajor problem in applications such as de novo genome assembly, metagenomics analysis and single nucleo

187 which in turn introduces new challenges for genome assembly methods.

188 ds the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotati

189 We report a second genome assembly obtained by a single cell genomics appro

190 We used genome assemblies of bread wheat and five diploid relati

191 ent-free strategy against eleven draft whole genome assemblies of E. coli O104:H4 German outbreak iso

192 with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat.

193 nd we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium S

194 re reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath.

195 We report the de novo whole-genome assemblies of the donkey and the Asiatic wild ass

196 pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Ch

197 ne our method with draft sequences to create genome assemblies of the mosquito disease vectors Aeaegy

198 We describe the draft genome assemblies of two white spruce genotypes, PG29 an

199 cs approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics

200 ltivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents o

201 ploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Pan

202 y-related taxa, obviating the need for draft genome assembly of all taxa of interest.

203 Here we present the first genome assembly of an extremophile, the first dipteran i

204 We report the high-quality genome assembly of approximately 16,000 complete nanochr

205 Metagenomic sequencing allowed draft genome assembly of dominant uncultivated community membe

206 parative analysis of a high quality finished genome assembly of Drechmeria coniospora, a model endopa

207 data from Drosophila melanogaster, a complex genome assembly of Homo sapiens and the low coverage San

208 We undertook a draft de novo genome assembly of horseweed by combining data from mult

209 Whole genome assembly of pooled reads showed that uncultured l

210 mposition of sugarcane genome as well as the genome assembly of S. spontaneum.

211 In this study, we compared a draft genome assembly of Salmonella enterica subsp. salamae st

212 We report a 729 Mbp genome assembly of the Calycopis cecrops, the first geno

213 Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.2

214 Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster

215 high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement a

216 Here we describe a high-quality genome assembly of the parents of the IL population.

217 is of such attributes, we present here a new genome assembly of the Philippine tarsier (Tarsius syric

218 Here, we present a complete genome assembly of the skin commensal yeast Malassezia s

219 Here we present a high-quality genome assembly of this species (1.37 Gb, scaffold N50 =

220 ivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.

221 A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any param

222 sting that they often result from inaccurate genome assemblies or gene models.

223 but is insufficient to generate high-quality genome assemblies or resolve most structural variation.

224 tively short read length limits their use in genome assembly or finishing.

225 f sequences not represented in the reference genome assembly or on standard SNP microarray platforms.

226 tau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals.

227 The human reference genome assembly plays a central role in nearly all aspec

228 uality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies

229 tering algorithm, our approach turns a whole genome assembly problem into a set of independent SV ass

230 chnologies have raised a challenging de novo genome assembly problem that is further amplified in rec

231 The genome assembly procedure we describe is fast, inexpensi

232 aps have not previously been used within the genome assembly process.

233 We present a hierarchical genome-assembly process (HGAP) for high-quality de novo

234 s been considerable progress in the field of genome assembly, producing high-quality de novo assembli

235 We evaluated the ability of multiple genome assembly programs to assemble bacterial genomes f

236 ool for genome assembly, SIMBA is a complete genome assemblies project management system, which can b

237 o inform studies of genome evolution, assist genome assembly projects and aid gene discovery and iden

238 While genome assembly projects have been successful in many ha

239 Genome assembly projects typically run multiple algorith

240 These difficulties often delay the complete genome assembly projects.

241 bstantial cost and effort required to finish genome assembly projects.

242 lows for population genetic, metagenomic and genome assembly provide automation of data conversion, a

243 In addition, the high quality of this genome assembly provides a clearer understanding of key

244 This genome assembly provides a draft of a scrambled genome a

245 Nevertheless, most recent genome assemblies remain incomplete and fragmented.

246 tool, but obtaining high quality eukaryotic genome assemblies remains a challenge, mostly due to the

247 Unfortunately, genome assembly remains a very difficult problem, made m

248 Open-source bacterial genome assembly remains inaccessible to many biologists

249 The genome assembly remains on many contigs, but gene space

250 Genome assembly, repeat detection, multiple sequence ali

251 A partial genome assembly, representing 24% of the total size, and

252 entification of bacterial pathogenicity - no genome assembly required.

253 h enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and ident

254 Analysis of the genome assembly reveals that the unitary chromosome aros

255 Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies p

256 k presents the most contiguous diploid human genome assembly so far, with extensive investigation of

257 chnologies have limited their use in de novo genome assembly, structural variation detection, and hap

258 ENA has faced a dramatic growth in genome assembly submission rates, data volumes and compl

259 of human sequences to sequences in non-human genome assemblies such as mouse and Nicotiana.

260 e browser and as a tool to compare different genome assembly, such as hg19 and hg38.

261 /or newer short-read sequence data and whole genome assembly techniques.

262 Genome assemblies that are accurate, complete and contig

263 to assess the gene space represented in the genome assemblies, the number of genes retrieved increas

264 ing JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1

265 he attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotat

266 Here, we review approaches to genome assembly, the nature of gaps or missing sequences

267 In genome assembly, the primary issue is how to determine u

268 Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database and as

269 alytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pi

270 hts into assembly composition and quality of genome assemblies through pairwise comparison of k-mers

271 Here, we use newly available reference genome assemblies to investigate phylogenetic relationsh

272 na-derived sequence data to polish the final genome assembly to 99.8% nucleotide accuracy when compar

273 e represents the most complete de novo human genome assembly to date.

274 Genome assembly tools based on the de Bruijn graph frame

275 Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome asse

276 ss (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotg

277 Recently, genome assemblies using Oxford Nanopore MinION data have

278 me engineering (CAGE) is a precise method of genome assembly using conjugation to hierarchically comb

279 challenges of generating a complete de novo genome assembly using current technologies and the impac

280 estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known ph

281 ase provides access to an updated version of genome assembly (v3) upon which all data integration is

282 ively mature technology that can be used for genome assembly validation.

283 Our study demonstrates that current genome assemblies vastly underestimate the complexity, a

284 ith defects in rhizoid growth, and a de novo genome assembly was generated to identify the mutant gen

285 Using crude whole-genome assemblies, we analyzed 25 isolates of Neisseria

286 E annotation methods are designed to work on genome assemblies, we sought to develop a method to prov

287 ther seven segments during influenza A virus genome assembly, we continued to use this HEF virus as a

288 ected markers from the genetic map and draft genome assembly were employed to screen for fosmid clone

289 n 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome ass

290 rable workflow management system for de novo genome assembly, which helps the user identify combinati

291 ferentially to gaps in the current reference genome assembly, which we resolved in this study.

292 nment steps, extensive homology searches, or genome assembly--which are time-consuming and labor-inte

293 tools are ushering in an era where complete genome assembly will become common for species with few

294 The high-quality great tit genome assembly will play an instrumental role in furthe

295 Hosted data range from genome assemblies with annotated gene features, transcri

296 sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error

297 ng data and improves the accuracy of de novo genome assembly with increasing coverage depth.

298 have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of

299 Furthermore, hybrid genome assembly with RTnS and HTS reads substantially im

300 rt robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo