title: Meta-aligner: long-read alignment based on genome statistics.
abstract: BACKGROUND
  Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners.
  
  
  RESULTS
  We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates statistics from reads and the reference genome automatically. Meta-aligner is implemented in C++ and runs in popular POSIX-like operating systems such as Linux.
  
  
  CONCLUSIONS
  Meta-aligner achieves high recall rates and precisions especially for long reads and high error rates. Also, it improves performance of alignment in the case of PacBio long-reads in comparison with traditional schemes.
authors.affiliation: Department of Electrical Engineering, Sharif University of Technology, Tehran, Azadi, Iran.
authors.forename: Damoon
authors.initials: D
authors.lastname: Nashta-Ali
authors.affiliation: Department of Electrical Engineering, Sharif University of Technology, Tehran, Azadi, Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Aliyari
authors.affiliation: Department of Computer Engineering, Sharif University of Technology, Azadi, Tehran, Iran.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Ahmadian Moghadam
authors.affiliation: Department of Electrical Engineering, Sharif University of Technology, Tehran, Azadi, Iran.
authors.forename: Mohammad Amin
authors.initials: MA
authors.lastname: Edrisi
authors.affiliation: Department of Computer Engineering, Sharif University of Technology, Azadi, Tehran, Iran.
authors.forename: Seyed Abolfazl
authors.initials: SA
authors.lastname: Motahari
authors.affiliation: Department of Electrical Engineering, Sharif University of Technology, Tehran, Azadi, Iran. khalaj@sharif.ir.
authors.forename: Babak
authors.initials: B
authors.lastname: Hossein Khalaj
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D056915:DNA Copy Number Variations; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004247:DNA
keywords: Alignment; Genome structure; Long-read sequencing; Repeat regions