Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Assembly by Reduced Complexity (ARC): a hybrid approach for targeted assembly of homologous sequences

Samuel S. Hunter, Robert T. Lyon, Brice A. J. Sarver, Kayla Hardwick, Larry J. Forney, Matthew L. Settles
doi: https://doi.org/10.1101/014662
Samuel S. Hunter
1 Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert T. Lyon
1 Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051,
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brice A. J. Sarver
1 Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051,
2 Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kayla Hardwick
2 Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Larry J. Forney
1 Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051,
2 Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Matthew L. Settles
1 Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051,
2 Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Analysis of High-throughput sequencing (HTS) data is a difficult problem, especially in the context of non-model organisms where comparison of homologous sequences may be hindered by the lack of a close reference genome. Current mapping-based methods rely on the availability of a highly similar reference sequence, whereas de novo assemblies produce anonymous (unannotated) contigs that are not easily compared across samples. Here, we present Assembly by Reduced Complexity (ARC) a hybrid mapping and assembly approach for targeted assembly of homologous sequences. ARC is an open-source project (http://ibest.github.io/ARC/) implemented in the Python language and consists of the following stages: 1) align sequence reads to reference targets, 2) use alignment results to distribute reads into target specific bins, 3) perform assemblies for each bin (target) to produce contigs, and 4) replace previous reference targets with assembled contigs and iterate. We show that ARC is able to assemble high quality, unbiased mitochondrial genomes seeded from 11 progressively divergent references, and is able to assemble full mitochondrial genomes starting from short, poor quality ancient DNA reads. We also show ARC compares favorably to de novo assembly of a large exome capture dataset for CPU and memory requirements; assembling 7,627 individual targets across 55 samples, completing over 1.3 million assemblies in less than 78 hours, while using under 32 Gb of system memory. ARC breaks the assembly problem down into many smaller problems, solving the anonymous contig and poor scaling inherent in some de novo assembly methods and reference bias inherent in traditional read mapping.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted February 07, 2015.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Assembly by Reduced Complexity (ARC): a hybrid approach for targeted assembly of homologous sequences
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Assembly by Reduced Complexity (ARC): a hybrid approach for targeted assembly of homologous sequences
Samuel S. Hunter, Robert T. Lyon, Brice A. J. Sarver, Kayla Hardwick, Larry J. Forney, Matthew L. Settles
bioRxiv 014662; doi: https://doi.org/10.1101/014662
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Assembly by Reduced Complexity (ARC): a hybrid approach for targeted assembly of homologous sequences
Samuel S. Hunter, Robert T. Lyon, Brice A. J. Sarver, Kayla Hardwick, Larry J. Forney, Matthew L. Settles
bioRxiv 014662; doi: https://doi.org/10.1101/014662

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4116)
  • Biochemistry (8819)
  • Bioengineering (6522)
  • Bioinformatics (23467)
  • Biophysics (11796)
  • Cancer Biology (9215)
  • Cell Biology (13327)
  • Clinical Trials (138)
  • Developmental Biology (7439)
  • Ecology (11416)
  • Epidemiology (2066)
  • Evolutionary Biology (15155)
  • Genetics (10439)
  • Genomics (14046)
  • Immunology (9174)
  • Microbiology (22164)
  • Molecular Biology (8815)
  • Neuroscience (47585)
  • Paleontology (350)
  • Pathology (1429)
  • Pharmacology and Toxicology (2492)
  • Physiology (3731)
  • Plant Biology (8082)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2221)
  • Systems Biology (6039)
  • Zoology (1253)