Literature DB >> 25392234

Do it yourself guide to genome assembly.

Bilal Wajid, Erchin Serpedin.   

Abstract

Bioinformatics skills required for genome sequencing often represent a significant hurdle for many researchers working in computational biology. This humble effort highlights the significance of genome assembly as a research area, focuses on its need to remain accurate, provides details about the characteristics of the raw data, examines some key metrics, emphasizes some tools and draws attention to a generic tutorial with example data that outlines the whole pipeline for next-generation sequencing. The article concludes by pointing out some major future research problems.
© The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Keywords:  Eulerian path; comparative assembly; de novo assembly; de-Bruijn graphs; genome assembly; next-generation sequencing

Mesh:

Year:  2014        PMID: 25392234     DOI: 10.1093/bfgp/elu042

Source DB:  PubMed          Journal:  Brief Funct Genomics        ISSN: 2041-2649            Impact factor:   4.241


  11 in total

1.  Whole genome sequencing and phylogenomic analyses of a novel glufosinate-tolerant Pseudomonas species.

Authors:  Wei Yee Wee; Xin Yi Chew; Sima Taheri; Xue Li Tan; Chee How Teo
Journal:  3 Biotech       Date:  2022-04-25       Impact factor: 2.893

Review 2.  Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases.

Authors:  Haseeb Nisar; Bilal Wajid; Samiah Shahid; Faria Anwar; Imran Wajid; Asia Khatoon; Mian Usman Sattar; Saima Sadaf
Journal:  Exp Biol Med (Maywood)       Date:  2021-09-15

Review 3.  The A, C, G, and T of Genome Assembly.

Authors:  Bilal Wajid; Muhammad U Sohail; Ali R Ekti; Erchin Serpedin
Journal:  Biomed Res Int       Date:  2016-05-10       Impact factor: 3.411

4.  Brassica napus Infected with Leptosphaeria maculans.

Authors:  Jin-Qi Ma; Li-Juan Wei; Ai Lin; Chao Zhang; Wei Sun; Bo Yang; Kun Lu; Jia-Na Li
Journal:  Genes (Basel)       Date:  2019-04-11       Impact factor: 4.096

5.  Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species.

Authors:  Adrián Casanova; Francesco Maroso; Andrés Blanco; Miguel Hermida; Néstor Ríos; Graciela García; Alice Manuzzi; Lorenzo Zane; Ana Verissimo; José-Luís García-Marín; Carmen Bouza; Manuel Vera; Paulino Martínez
Journal:  BMC Genomics       Date:  2021-03-02       Impact factor: 3.969

6.  Profiling of RNA Viruses in Biting Midges (Ceratopogonidae) and Related Diptera from Kenya Using Metagenomics and Metabarcoding Analysis.

Authors:  Solomon K Langat; Fredrick Eyase; Wallace Bulimo; Joel Lutomiah; Samuel O Oyola; Mabel Imbuga; Rosemary Sang
Journal:  mSphere       Date:  2021-10-13       Impact factor: 4.389

Review 7.  Population Genomic Approaches for Weed Science.

Authors:  Sara L Martin; Jean-Sebastien Parent; Martin Laforest; Eric Page; Julia M Kreiner; Tracey James
Journal:  Plants (Basel)       Date:  2019-09-19

Review 8.  The Value of Reference Genomes in the Conservation of Threatened Species.

Authors:  Parice Brandies; Emma Peel; Carolyn J Hogg; Katherine Belov
Journal:  Genes (Basel)       Date:  2019-10-25       Impact factor: 4.096

9.  Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly.

Authors:  Sudeep Ghimire; Chayan Roy; Supapit Wongkuna; Linto Antony; Abhijit Maji; Mitchel Chan Keena; Andrew Foley; Joy Scaria
Journal:  mSystems       Date:  2020-02-04       Impact factor: 6.496

10.  An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae.

Authors:  José Córdoba-Caballero; Pedro Seoane; Fernando M Jabato; James R Perkins; Manuel Manchado; M Gonzalo Claros
Journal:  Sci Rep       Date:  2020-11-26       Impact factor: 4.379

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