ARYANA: Aligning Reads by Yet Another Approach

Abstract

MotivationAlthough there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment.ContributionWe introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine.AvailabilityARYANA with complete source code can be obtained from http://github.com/aryana-aligner

Alignment of Single-Molecule Sequencing Reads by Enhancing the Accuracy and Efficiency of Locality-Sensitive Hashing

“…The algorithmic approach of Aryana for aligning short reads is already published [15]. Briefly, it splits the reference genome into equal size intervals called tags .…”

“…Finally, it reports the least penalized alignment (or a user-defined number of best alignments). More details are provided in the previous article [15].…”

“…This is to ensure at least one tag will cover the whole genomic region of each read. The set of selected tag sizes is {2 9 , 2 11 , 2 13 , 2 15 } based on the distribution of SMS reads, obtained from real Pacific Biosciences and Oxford Nanopore datasets. Each tag is assigned a unique label.…”

ARYANA-BS: Context-Aware Alignment of Bisulfite-Sequencing Reads

“…ARYANA-BS is an enhancement of our conventional short-read aligner ARYANA [11], which performs context-aware alignment of BS reads. To better describe ARYANA-BS, we need to have a quick glance over how ARYANA works, and then review what enhancements are made to build ARYANA-BS.…”

“…In this article, we introduce ARYANA-BS, a novel short read aligner for bisulfite sequencing that builds upon our previous work on the conventional short read aligner, ARYANA [11]. Unlike many existing methods that rely on adapting reads and/or references, ARYANA-BS incorporates specific treatments for BS reads during the alignment process.…”