The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

نویسندگان

چکیده

The quality of genome assemblies has improved rapidly in recent years due to continual advances sequencing technology, assembly approaches, and control. In the field molecular ecology, this led development exceptional that will be important long-term resources for broader studies into ecological, conservation, evolutionary, population genomics naturally occurring species. Moreover, extent which a single reference represents diversity within species varies: pan-genomes become increasingly ecological resources, particularly systems found have considerable presence-absence variation their functional content. Here, we highlight technology raised bar provide guidance on standards achieve genomes. Key recommendations include following: (a) Genome should long-read except rare cases where it is effectively impossible acquire adequately preserved samples needed high weight DNA standards. (b) At least one scaffolding approach included with such as Hi-C or optical mapping. (c) carefully evaluated, may involve utilising short read data polishing, error correction, k-mer analyses, estimating percent reads map back an assembly. Finally, most valuable if all methods are made publicly available utility further verified through examples. While these based current anticipate future push ecology community continue adopt new approaches attain highest assemblies.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Modernizing Reference Genome Assemblies

Modernizing Reference Genome Assemblies Deanna M. Church*, Valerie A. Schneider, Tina Graves, Katherine Auger, Fiona Cunningham, Nathan Bouk, Hsiu-Chuan Chen, Richa Agarwala, William M. McLaren, Graham R.S. Ritchie, Derek Albracht, Milinn Kremitzki, Susan Rock, Holland Kotkiewicz, Colin Kremitzki, Aye Wollam, Lee Trani, Lucinda Fulton, Robert Fulton, Lucy Matthews, Siobhan Whitehead, Will Chow,...

متن کامل

the effects of changing roughness on the flow structure in the bends

flow in natural river bends is a complex and turbulent phenomenon which affects the scour and sedimentations and causes an irregular bed topography on the bed. for the reason, the flow hydralics and the parameters which affect the flow to be studied and understand. in this study the effect of bed and wall roughness using the software fluent discussed in a sharp 90-degree flume bend with 40.3cm ...

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de ...

متن کامل

Whole Genome Assemblies of the Drosophila and Human Genomes

Shotgun sequence assembly is a classic inverse problem: given a set of segments randomly sampled from a target sequence, the problem is to reconstruct the target. Early programs for this problem assisted a user by finding potential overlapping segments which were then assembled by hand. As the programs became progressively more sophisticated the problem was completely solved by the software but...

متن کامل

the effect of consciousness-raising activities on learning grammatical structures by iranian guidance school efl learners

abstract the first purpose of this study was to investigate the effect of consciousness-raising (c-r) activities on learning grammatical structures (simple present tense in this case) by iranian guidance school efl learners. the second one was to investigate the effect of gender on learning the simple present tense through c-r activities and tasks. finally, this study aimed to investigate the ...

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

ژورنال

عنوان ژورنال: Molecular Ecology Resources

سال: 2021

ISSN: ['1755-0998', '1755-098X']

DOI: https://doi.org/10.1111/1755-0998.13312