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Combining de novo and reference-guided assembly with scaffold_builder

Genivaldo GZ Silva, Bas E Dutilh, T Matthews, Keri Elkins, Robert Schmieder, Elizabeth A Dinsdale, Robert A Edwards
2013 Source Code for Biology and Medicine  
Scaffold_builder is written in Python and is available at http://edwards.sdsu.edu/scaffold_builder.  ...  A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded.  ...  Acknowledgements The authors thank Anca Segall and her lab for providing the S. Typhimurium LT2 G455 and S.  ... 
doi:10.1186/1751-0473-8-23 pmid:24267787 pmcid:PMC4177539 fatcat:4w5gfasagreuhjninngttgvk6i

Metagenomic Assembly: Overview, Challenges and Applications

Jay S Ghurye, Victoria Cepeda-Espinoza, Mihai Pop
2016 The Yale Journal of Biology and Medicine  
Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment.  ...  In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field.  ...  Finally, e-RGA [21] performs de novo and reference guided assembly independently first and then merges two assemblies later using a novel data structure called merge graph to avoid mis-assemblies and  ... 
pmid:27698619 pmcid:PMC5045144 fatcat:ztzpyytwoba5rj2v4eid4uwx24

Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

Kevin J. Tsai, Mei-Yeh Jade Lu, Kai-Jung Yang, Mengyun Li, Yuchuan Teng, Shihmay Chen, Maurice S. B. Ku, Wen-Hsiung Li
2016 Scientific Reports  
We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of  ...  To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size.  ...  This study was supported by Innovative Translational Agricultural Research Program and by Academia Sinica, Taiwan (AS-102-SS-A13).  ... 
doi:10.1038/srep35076 pmid:27734962 pmcid:PMC5062080 fatcat:uf4fwlurfnhdfocfkdhrvwwrce

GRACY: a tool for analysing human cytomegalovirus sequence data

Salvatore Camiolo, Nicolás M Suárez, Antonia Chalka, Cristina Venturini, Judith Breuer, Andrew J Davison
2020 Virus Evolution  
GRACy automates and integrates modules for read filtering, genotyping, genome assembly, genome annotation, variant analysis and data submission.  ...  GRACy is distributed under a GPL 3.0 license and is freely available at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset.  ...  Joseph Hughes and Dr.  ... 
doi:10.1093/ve/veaa099 pmid:33505707 pmcid:PMC7816668 fatcat:xu7nf2rkujfwlfr77dxry5aqqi

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Bas E Dutilh, Cristiane C Thompson, Ana CP Vicente, Michel A Marin, Clarence Lee, Genivaldo GZ Silva, Robert Schmieder, Bruno GN Andrade, Luciane Chimetto, Daniel Cuevas, Daniel R Garza, Iruka N Okeke (+7 others)
2014 BMC Genomics  
Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs),  ...  Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses  ...  BED is supported by the Dutch Science foundation (NWO) Veni grant 016.111.075 and CAPES/BRASIL. ACPV, CCT, MAM and BNA are supported by CAPES, CNPq and IOC-FIOCRUZ.  ... 
doi:10.1186/1471-2164-15-654 pmid:25096633 pmcid:PMC4141962 fatcat:h2dyysezhbgq3ji5z7wxrpdw2a