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Extreme Scale De Novo Metagenome Assembly

Evangelos Georganas, Rob Egan, Steven Hofmeyr, Eugene Goltsman, Bill Arndt, Andrew Tritt, Aydin Buluc, Leonid Oliker, Katherine Yelick
2018 SC18: International Conference for High Performance Computing, Networking, Storage and Analysis  
This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code.  ...  De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics.  ...  ABySS [44] was the first de novo assembler written in MPI that also exhibits strong scaling.  ... 
doi:10.1109/sc.2018.00013 fatcat:zy4gfufkjbhzfm5m5kvled66ly

Extreme Scale De Novo Metagenome Assembly [article]

Evangelos Georganas, Rob Egan, Steven Hofmeyr, Eugene Goltsman, Bill Arndt, Andrew Tritt, Aydin Buluc, Leonid Oliker, Katherine Yelick
2018 arXiv   pre-print
Moreover, MetaHipMer scales efficiently to large concurrencies and is able to assemble previously intractable grand challenge metagenomes.  ...  In this paper, we introduce the MetaHipMer pipeline, a high-quality and high-performance metagenome assembler that employs an iterative de Bruijn graph approach.  ...  ARTIFACT DESCRIPTION APPENDIX: EXTREME SCALE DE NOVO METAGENOME ASSEMBLY A.  ... 
arXiv:1809.07014v1 fatcat:l4sl6nmkwzh5bewd3h5jxo3xre

HipMer

Evangelos Georganas, Aydın Buluç, Jarrod Chapman, Steven Hofmeyr, Chaitanya Aluru, Rob Egan, Leonid Oliker, Daniel Rokhsar, Katherine Yelick
2015 Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '15  
This work presents HipMer, the first high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code.  ...  De novo whole genome assembly reconstructs genomic sequences from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics.  ...  ABySS [25] was the first de novo assembler written in MPI that also exhibits strong scaling.  ... 
doi:10.1145/2807591.2807664 dblp:conf/sc/GeorganasBCHAEO15 fatcat:sdqi4brqzrag3pmuidaj7z3hfa

Tackling soil diversity with the assembly of large, complex metagenomes

Adina Chuang Howe, Janet K. Jansson, Stephanie A. Malfatti, Susannah G. Tringe, James M. Tiedje, C. Titus Brown
2014 Proceedings of the National Academy of Sciences of the United States of America  
The main challenge for metagenomic applications of de novo assembly is that current assembly tools do not scale to the high diversity and large volume of metagenomic data.  ...  We present approaches that make de novo assembly of complex metagenomes more accessible.  ... 
doi:10.1073/pnas.1402564111 pmid:24632729 pmcid:PMC3977251 fatcat:xbdr23kcmneyppbvuidx5wfjie

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

Maxime Borry, Alexander Hübner, Adam B. Rohrlach, Christina Warinner
2021 PeerJ  
Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.  ...  DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads.  ...  ACKNOWLEDGEMENTS We thank Nigel Bean and Jonathon Tuke for extremely useful discussions. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.11845 fatcat:mrlsgow4onhz3fv4z6s32yxhmq

A novice's guide to analyzing NGS-derived organelle and metagenome data

Hae Jung Song, JunMo Lee, Louis Graf, Mina Rho, Huan Qiu, Debashish Bhattacharya, Hwan Su Yoon
2016 ALGAE  
We focus specifically on the analysis of organelle genome and metagenome data and describe the current bioinformatic pipelines suited for this purpose.  ...  Li et al. (2015) MetaVelvet http://metavelvet.dna.bio.keio.ac.jp/ An extension of Velvet assembler for de novo metagenome as- sembly.  ...  For these reasons, major de novo assemblers, which were designed to assemble single or clonal genomes, are not suited to the assembly of metagenomes with abundant heterogeneous sequences, and thus, their  ... 
doi:10.4490/algae.2016.31.6.5 fatcat:dvyu3ggpjjhcnizbmjoz6r47w4

RNA-CODE: A Noncoding RNA Classification Tool for Short Reads in NGS Data Lacking Reference Genomes

Cheng Yuan, Yanni Sun, Ali Torkamani
2013 PLoS ONE  
The classification results can be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively.  ...  The experimental results of applying RNA-CODE to RNA-seq of Arabidopsis and a metagenomic data set sampled from human guts demonstrate that RNA-CODE competes favorably in both sensitivity and specificity  ...  In this work, the de novo assembly programs are applied to RNA-seq data of non-model organisms or metagenomic data.  ... 
doi:10.1371/journal.pone.0077596 pmid:24204885 pmcid:PMC3808423 fatcat:lprc3bsmdnhinbmnyeogrto3gu

Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing

Federica Cattonaro, Alessandro Spadotto, Slobodanka Radovic, Fabio Marroni
2018 F1000Research  
of de novo reconstruction of the whole metagenome or a set of genes of interest.  ...  Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct de novo—even partially—the metagenome.  ...  Acknowledgments The authors would like to thank Dr Loretta Bolgan for fruitful scientific discussions and Corvelva (non-profit association, Veneto, Italy) to give us the permission to use their own metagenome  ... 
doi:10.12688/f1000research.16804.1 pmid:32185014 pmcid:PMC7059852 fatcat:77z5homthzaffdhq2i6a6o3tga

Assembling large, complex environmental metagenomes [article]

Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti, Susannah G. Tringe, James M. Tiedje, C. Titus Brown
2012 arXiv   pre-print
De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources.  ...  We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils.  ...  The main challenge for metagenomic applications of de novo assembly is that current assembly tools do not scale to the high diversity and large volume of metagenomic data: metagenomes from rumen, human  ... 
arXiv:1212.2832v2 fatcat:6fccscbycjfljg6rfyzthbsprq

Assembling Metagenomes, One Community At A Time [article]

Andries Johannes van der Walt, Marc Warwick Van Goethem, Jean-Baptiste Ramond, Thulani Peter Makhalanyane, Oleg Reva, Don Arthur Cowan
2017 bioRxiv   pre-print
Results: To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as  ...  However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data.  ...  To this end, numerous metagenome assembly tools 53 (assemblers) have been developed, the vast majority of which assemble sequences in de novo 54 fashion.  ... 
doi:10.1101/120154 fatcat:p3ix76gu4zcutnjbmkttn634ou

MinYS: mine your symbiont by targeted genome assembly in symbiotic communities

Cervin Guyomar, Wesley Delage, Fabrice Legeai, Christophe Mougel, Jean-Christophe Simon, Claire Lemaitre
2020 NAR Genomics and Bioinformatics  
Then, this draft assembly is completed using the whole metagenomic readset in a de novo manner.  ...  We present MinYS, a targeted assembly approach to assemble a particular genome of interest from such metagenomic data.  ...  a de novo metagenomic assembly [MEGAHIT (11) ] followed by BLAST-based con-tig filtering.  ... 
doi:10.1093/nargab/lqaa047 pmid:33575599 pmcid:PMC7671366 fatcat:kravna427bdcjlbxvwozmr3oge

MinYS: Mine Your Symbiont by targeted genome assembly in symbiotic communities [article]

Cervin Guyomar, Wesley Delage, Fabrice Legeai, Christophe Mougel, Jean-Christophe Simon, Claire Lemaitre
2019 biorxiv/medrxiv   pre-print
Then, this draft assembly is completed using the whole metagenomic readset in a de novo manner.  ...  We present MinYS, a targeted assembly approach to assemble one particular genome of interest from such metagenomic data.  ...  a de novo metagenomic assembly [MEGAHIT (11) ] followed by BLAST-based con-tig filtering.  ... 
doi:10.1101/2019.12.13.875021 fatcat:rtu2cldm55hg7exwybueuwc2du

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community

Sheila Podell, Joanne B Emerson, Claudia M Jones, Juan A Ugalde, Sue Welch, Karla B Heidelberg, Jillian F Banfield, Eric E Allen
2013 The ISME Journal  
Microbial community succession was examined over a two-year period using spatially and temporally coordinated water chemistry measurements, metagenomic sequencing, phylogenetic binning and de novo metagenomic  ...  assembly in the extreme hypersaline habitat of Lake Tyrrell, Victoria, Australia.  ...  rRNA gene amplification, metagenomic sequencing and de novo assembly of habitat-specific reference genomes for Archaea, bacteria, and viruses Narasingarao et al., 2012; Emerson et al., 2013; Heidelberg  ... 
doi:10.1038/ismej.2013.221 pmid:24335829 pmcid:PMC3996697 fatcat:ecgxkabgwbb4lbidxtdibtar54

SpaRC: Scalable Sequence Clustering using Apache Spark [article]

Lizhen Shi, Xiandong Meng, Elizabeth Tseng, Michael Mascagni, Zhong Wang
2018 bioRxiv   pre-print
De novo assembling these data requires an ideal solution that both scales with data size and optimizes for individual gene or genomes.  ...  SpaRC produces high clustering performance on transcriptomics and metagenomics test datasets from both short read and long read sequencing technologies.  ...  For a comprehensive review of de novo assembly algorithms please refer 44 to [25] .  ... 
doi:10.1101/246496 fatcat:3qdr2rvcmzcbxiqrjjlm3lh5ry

SpaRC: scalable sequence clustering using Apache Spark

Lizhen Shi, Xiandong Meng, Elizabeth Tseng, Michael Mascagni, Zhong Wang, Inanc Birol
2018 Bioinformatics  
An ideal solution would both scale and produce optimal accuracy for individual genes or genomes.  ...  Assembly of these data sets requires tradeoffs between scalability and accuracy. Current assembly methods optimized for scalability often sacrifice accuracy and vice versa.  ...  For a comprehensive review of de novo assembly algorithms please refer 44 to [25] .  ... 
doi:10.1093/bioinformatics/bty733 pmid:30816928 fatcat:id5vvsqnova6nchis5kgqaiera
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