ライフサイエンスコーパス: genome assembly

1 been hampered because of a highly fragmented genome assembly.

2 f DNA sequence not included in the reference genome assembly.

3 nbred lines in addition to the B73 reference genome assembly.

4 ze error correction and consequently improve genome assembly.

5 ructed by short read mapping to a particular genome assembly.

6 , to evaluate the genetic alignment with the genome assembly.

7 y verify and potentially improve the herring genome assembly.

8 regions are missing from the current chicken genome assembly.

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

10 llected during mutant mapping to improve the genome assembly.

11 ave now been extended to the current chicken genome assembly.

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

13 xpertise on methodologies and techniques for genome assembly.

14 ntal-specific manner during a second wave of genome assembly.

15 reaction (RT-qPCR), 14 of which resulted in genome assembly.

16 d assembled a novel, high-quality D. suzukii genome assembly.

17 000 high-confidence gene models from a wheat genome assembly.

18 ological insight enabled by chromosome-level genome assemblies.

19 n improve the contiguity and completeness of genome assemblies.

20 for whole-genome and targeted data) and from genome assemblies.

21 or efficiently transforming variants between genome assemblies.

22 sed regions of segmental duplications within genome assemblies.

23 ogous contigs of equivalent quality to whole genome assemblies.

24 used to generate efficient chromosome-level genome assemblies.

25 complementary metric to BUSCO for assessing genome assemblies.

26 k-mer content to that of publicly available genome assemblies.

27 y pose a challenge while generating accurate genome assemblies.

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

29 lizing synteny between two or more annotated genome assemblies.

30 ainst a vast collection of quality reference genome assemblies.

31 of dramatically improving the contiguity of genome assemblies.

32 hensive validation and refinement of de novo genome assemblies.

33 mprovements in the contiguity and quality of genome assemblies.

34 er repeat resolution and far more contiguous genome assemblies.

35 roduced during the annotation of prokaryotic genome assemblies.

36 Two species with haploid genome assemblies ~150 Mb are among the largest in Agari

37 BGC is encoded within a single contig in the genome assembly, a condition that is violated for most s

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

39 data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling

40 raph-based approaches in solving sequence to genome assembly alignment problem.

41 d procedures used for pathogen discovery and genome assembly, along with the most common challenges a

42 Two draft genome assemblies already exist for this species but con

43 Based on de novo genome assemblies and additional whole-genome resequenci

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

45 Our genome assemblies and annotations also provide comprehen

46 the RefSeq database to explore how deposited genome assemblies and annotations are changing over time

47 Here we report reference-grade genome assemblies and annotations for G. hirsutum access

48 Generating high-quality genome assemblies and annotations for many aquatic speci

49 We report reference-quality genome assemblies and annotations for two accessions of

50 erences across multiple species to improving genome assemblies and annotations.

51 ine shared and variable TE insertions across genome assemblies and applied this method to four maize

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

53 Genomics approaches, including de novo genome assemblies and gene annotations for the populatio

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

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

56 We generate high quality de novo genome assemblies and population genomic resources for m

57 dation for anchoring and orienting annotated genome assemblies and positional cloning of candidate ge

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

59 haploid nature, it is frequently absent from genome assemblies and remains enigmatic.

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

61 Here, we used publicly available genome assemblies and small RNA sequencing data sets to

62 e list of contaminant sequences in bacterial genome assemblies and the proteins associated with them.

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

64 gies have already found many applications in genome assembly and analysis.

65 3 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in

66 he GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, mad

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

68 A de novo, high-quality genome assembly and annotation for E. curvula have been

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

70 c landscape, we produced an improved de novo genome assembly and annotation of F. virguliforme using

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

72 tainable over time, and cover all aspects of genome assembly and annotation projects from start to fi

73 A chromosome-level genome assembly and annotation were established for one

74 n the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome r

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

76 g-by-sequencing approach requires an ordered genome assembly and cannot be used with fragmented, un-s

77 Genome assembly and comparison of read coverage in male

78 type transition, we improved the fragmented genome assembly and constructed a chromosome-level genom

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

80 We present a complete B. malayi genome assembly and define Nigon elements shared with C.

81 Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that U

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

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

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

85 circa 400 mya, to obtain a whole chromosome genome assembly and explore the chromatin landscape and

86 quence reads, they provide a useful tool for genome assembly and for discovering structural variation

87 nding of the underlying mechanisms governing genome assembly and function.

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

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

90 st a sequential NC binding mechanism for Gag-genome assembly and identify a potential RNA Achilles' h

91 We generate an improved reference genome assembly and identify genes under positive and pu

92 n greatly decrease the complexity of de novo genome assembly and large structural variation identific

93 Here, we report a high-quality genome assembly and linkage map for the Antarctic blackf

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

95 s, nanopore quality metrics were defined for genome assembly and mutation analysis.

96 ) at 4-16 weeks postpartum, then analyzed by genome assembly and novel motif-based genotyping in 12 h

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

98 c workflows frequently make use of automated genome assembly and protein clustering tools.

99 By generating a new genome assembly and re-sequencing 453 genomes, we uncove

100 An important assessment prior to genome assembly and related analyses is genome profiling

101 pproach is applicable to any organism with a genome assembly and requires no a priori assumptions.

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

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

104 sed the availability of genomic data, phased genome assembly and structural variant (SV) analyses are

105 igh quality long-read based ~886 Mbp nuclear genome assembly and transcriptome data from the dominant

106 sion measurements, new sequencing platforms, genome assembly and variation, and long and linked reads

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

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

109 poses fundamental challenges for sequencing, genome assembly, and automated annotation of genes and p

110 scaffolding, cost-effective diploid de novo genome assembly, and other long DNA sequencing applicati

111 In genomics, generating a high-quality genome assembly/annotation has become an indispensable t

112 These genome assemblies are commonly assessed using statistics

113 We demonstrate that current Cannabis genome assemblies are incomplete, with ~10% missing, 10-

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

115 D now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous ref

116 nd reproducible pipeline that takes multiple genome assemblies as FASTA and compares them to several

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

118 e nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quali

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

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

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

122 mster ovary (CHO) cell lines with only draft genome assemblies available.

123 Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a d

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

125 ong-range assays have revolutionized de novo genome assembly by automating the reconstruction of refe

126 Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, Bio

127 ology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in

128 mic structural variation, a single reference genome assembly cannot capture the full complement of se

129 gh levels of heterozygosity present a unique genome assembly challenge and can adversely impact downs

130 o improve the completeness and contiguity of genome assemblies compared to conventional assembly.

131 Recent efforts have yielded genome assemblies consisting of thousands of unordered s

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

133 The genome assembly contained 34,105 expressed genes, of whi

134 For example, the number of vertebrate genome assemblies currently in the NCBI (National Center

135 RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map.

136 xity of the wheat genome(1), and the lack of genome-assembly data for multiple wheat lines(2,3).

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

138 Recent genome assembly efforts in the large-genome Triticeae cr

139 ables users to identify and report potential genome assembly errors and structural variants.

140 hin the coding regions of GPI-CWP genes, our genome assembly establishes a high-quality reference set

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

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

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

144 alyzed with a two-step pipeline: (i) de novo genome assembly, followed by (ii) read remapping.

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

146 ic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species:

147 The genome assemblies for multiple cultivated accessions and

148 baicalensis is also useful for improving the genome assemblies for other members of the mint family a

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

150 cing and Hi-C scaffolding to produce de novo genome assemblies for two wild strains of Drosophila mel

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

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

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

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

155 egy, we produced a completely phased de novo genome assembly for each haplotype of an individual of P

156 It is the first genome assembly for larch species in addition to only fi

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

158 Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in l

159 e first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original geneti

160 Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss)

161 enomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora We obta

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

163 We present a draft genome assembly for the tropical liverwort, Marchantia i

164 nment search tool (BLAST) search against the genome assembly for their particular polyploid crop.

165 We produce a high-quality genome assembly for this species and characterize its ge

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

167 high-resolution de novo chromosome-assigned genome assembly for V. komodoensis using a hybrid approa

168 Complete and accurate genome assemblies form the basis of most downstream geno

169 ways databases, and synteny among the newest genome assemblies from eight species can be viewed throu

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

171 Whole genome assemblies from these data remain high time- and

172 and would be an expedient choice when whole genome assembly from the reads is either not feasible, t

173 ss this latter issue, we combine an improved genome assembly from the unicellular red alga Porphyridi

174 in the Solanaceae family, but a high-quality genome assembly from this group is presently missing.

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

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

177 GCs in a single contig, the structure of the genome assembly graph often provides clues on how to com

178 Graph-based representation of genome assemblies has been recently used in different co

179 This single fly genome assembly has a N50 of 26 Mb, a length that encomp

180 The availability of this genome assembly has allowed us to identify regions assoc

181 Hybrid genome assembly has emerged as an important technique in

182 The wild soybean genome assembly has wide applications in comparative gen

183 New genome assemblies have been arriving at a rapidly increa

184 ome assembly program, and address how animal genome assemblies have improved since 2016.

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

186 We discuss genome assembly improvements/degradations in 57 cases wh

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

188 highlights the utility of this high-quality genome assembly in deciphering agriculturally important

189 This is the first reported mitochondrial genome assembly in the genus Chenopodium.

190 Shasta produced a complete haploid human genome assembly in under 6 h on a single commercial comp

191 curately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 referen

192 Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencin

193 and Hi-C technologies to anchor the ~1.47-Gb genome assembly into 18 pseudochromosomes.

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

195 A high quality genome assembly is a vital first step for the study of a

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

197 Accurate genome assembly is hampered by repetitive regions.

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

199 se signals generated by incomplete reference genome assembly, location in low-complexity regions, bio

200 that filtering out small contigs from draft genome assemblies may mitigate the issue of contaminatio

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

202 We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that incr

203 create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indici

204 genome completeness assessment utilizing 246 genome assemblies of fungi.

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

206 this study, we leveraged the availability of genome assemblies of multiple individuals in many specie

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

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

209 ns from the Brassicaceae, including multiple genome assemblies of the same species where available (t

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

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

212 Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus virid

213 Here we report the chromosome-level genome assembly of a Xenia species of fast-growing soft

214 d at hunting for active prophages from whole genome assembly of bacteria.

215 The high-quality genome assembly of C. pomonella informs the genetic basi

216 Here, we report a chromosome-level genome assembly of C. salicifolius, comprising 820.1 Mb

217 assembly and constructed a chromosome-level genome assembly of C. tropicalis by employing PacBio seq

218 y with a total size of 695.36 Mb and a draft genome assembly of Calycanthus chinensis.

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

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

221 We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), contain

222 Here, we report a chromosome-level genome assembly of L. japonica, comprising nine pseudoch

223 We generate a chromosome-scale genome assembly of mango, providing a reference genome f

224 We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly

225 we present a high-quality, chromosome-scale genome assembly of P. trifoliata.

226 Here, we analyze a high-quality genome assembly of Pyropia yezoensis to elucidate the in

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

228 We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for

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

230 Although the de novo genome assembly of the giant panda is available, current

231 hort-read metagenomic sequencing and de novo genome assembly of the human gut microbiome can yield dr

232 By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis,

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

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

235 on the recent availability of a high quality genome assembly of the planarian model species Schmidtea

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

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

238 hromatic SVs from 14 Drosophila melanogaster genome assemblies, of which ~40% are invisible to high s

239 ltiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, a

240 s and effective choices for each step of the genome assembly pipeline using nanopore sequence data.

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

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

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

244 The genome assembly procedure we describe is fast, inexpensi

245 used in post-processing step and not in the genome assembly process itself.

246 6, identify the most commonly used bacterial genome assembly program, and address how animal genome a

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

248 Currently, most genome assembly projects focus on contigs and scaffolds

249 While genome assembly projects have been successful in many ha

250 Recent genome assembly projects have relied on a combination of

251 h they have been a regular feature of modern genome assembly projects, optical maps have been mainly

252 Haplotype-resolved or phased genome assembly provides a complete picture of genomes a

253 relying solely on contiguity as a measure of genome assembly quality as well as current alternative m

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

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

256 This genome assembly represents key resources for future rubb

257 The AalbF2 genome assembly represents the most up-to-date collectiv

258 entification of bacterial pathogenicity - no genome assembly required.

259 porating data analyzed on an older reference genome assembly requires transforming the coordinates an

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

261 ion analyses and comparisons of high-quality genome assemblies revealed that these two species displa

262 A new genome assembly reveals how repurposing of developmental

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

264 We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque

265 The rheMacS genome assembly serves as an ideal reference for future

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

267 offers an efficient tool to complement whole genome assembly software.

268 In such genomes, assembly software produces incomplete and fragm

269 ng project or with respect to ultimate whole genome assembly strategies.

270 omeres with newly generated chromosome-level genome assemblies suggests two distinct mechanisms of ch

271 lopments in gene editing, speed breeding and genome assembly techniques mean that the challenges asso

272 reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasin

273 Here we present a human genome assembly that surpasses the continuity of GRCh38(

274 three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Sv

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

276 We used 20 de novo genome assemblies to probe the speciation history and ar

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

278 0 read length 11.8 kb) and generated de novo genome assembly to the level of pseudochromosomes contai

279 The availability of a high-quality genome assembly together with companion genomic and tran

280 We obtained a genome assembly totaling 227.6 Mb of the estimated almon

281 drugs that inhibit viral entry, endocytosis, genome assembly, translation, and replication.

282 Recently, genome assemblies using Oxford Nanopore MinION data have

283 we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequen

284 De novo genome assembly using CCS reads alone produced a contigu

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

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

287 In 2016, a draft herring genome assembly was published.

288 Taken together, the highly contiguous genome assembly we present opens unexplored avenues for

289 than 800 Bcc and Burkholderia gladioli whole-genome assemblies, we constructed phylogenies with expli

290 To enable rapid human genome assembly, we present Shasta, a de novo long-read

291 Using a highly contiguous genome assembly, we show that gene expression is balance

292 Several tools, from base-calling to genome assembly, were ported and benchmarked on an Andro

293 These genome assemblies will provide a basis for functional ge

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

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

296 Using new genome assemblies with substantially higher contiguity t

297 e, we present a chromosome-level wintersweet genome assembly with a total size of 695.36 Mb and a dra

298 A comparison between the herring genome assembly with other high-quality assemblies from

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

300 Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer

301 dom sequencing approach coupled with de novo genome assembly within a customized data analysis workfl