Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

dc.contributor.author Howe, Adina
dc.contributor.author Howe, Adina
dc.contributor.author Chain, Patrick
dc.contributor.department Agricultural and Biosystems Engineering
dc.date 2018-02-16T17:37:46.000
dc.date.accessioned 2020-06-29T22:41:34Z
dc.date.available 2020-06-29T22:41:34Z
dc.date.copyright Thu Jan 01 00:00:00 UTC 2015
dc.date.issued 2015-07-09
dc.description.abstract <p>Metagenomic investigations hold great promise for informing the genetics, physiology, and ecology of environmental microorganisms. Current challenges for metagenomic analysis are related to our ability to connect the dots between sequencing reads, their population of origin, and their encoding functions. Assembly-based methods reduce dataset size by extending overlapping reads into larger contiguous sequences (contigs), providing contextual information for genetic sequences that does not rely on existing references. These methods, however, tend to be computationally intensive and are again challenged by sequencing errors as well as by genomic repeats While numerous tools have been developed based on these methodological concepts, they present confounding choices and training requirements to metagenomic investigators. To help with accessibility to assembly tools, this review also includes an IPython Notebook metagenomic assembly tutorial. This tutorial has instructions for execution any operating system using Amazon Elastic Cloud Compute and guides users through downloading, assembly, and mapping reads to contigs of a mock microbiome metagenome. Despite its challenges, metagenomic analysis has already revealed novel insights into many environments on Earth. As software, training, and data continue to emerge, metagenomic data access and its discoveries will to grow.</p>
dc.description.comments <p>This article was published in <em>Frontiers in Microbiology</em> 6 (2015): 678, doi:<a href="http://dx.doi.org/10.3389/fmicb.2015.00678" target="_blank">10.3389/fmicb.2015.00678</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/abe_eng_pubs/648/
dc.identifier.articleid 1931
dc.identifier.contextkey 7312519
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath abe_eng_pubs/648
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/1437
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/abe_eng_pubs/648/2015_Howe_ChallengesOpportunities.pdf|||Sat Jan 15 01:23:02 UTC 2022
dc.source.uri 10.3389/fmicb.2015.00678
dc.subject.disciplines Agriculture
dc.subject.disciplines Bioresource and Agricultural Engineering
dc.subject.disciplines Microbiology
dc.subject.keywords metagenomes
dc.subject.keywords assembly
dc.subject.keywords review
dc.subject.keywords challenges
dc.subject.keywords tutorial
dc.title Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication e2017bbe-ba62-4969-946e-aaf072d8bb4f
relation.isOrgUnitOfPublication 8eb24241-0d92-4baf-ae75-08f716d30801
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