title: Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics.
abstract: Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes. Two million simulated read pairs of various sizes (36bp, 50bp, 72bp, 100bp, 125bp, 150bp, 200bp, 250bp and 300bp) were aligned. Specific alignment features such as sensitivity of mapping, percentage of properly paired reads, alignment time and effect of tandem repeats on incorrectly mapped reads were evaluated. BWA showed faster alignment followed by Bowtie2 and Smalt. NovoAlign and Stampy were comparatively slower. Most of the aligners showed high sensitivity towards long reads (>100bp) mapping. On the other hand NovoAlign showed higher sensitivity towards both short reads (36bp, 50bp, 72bp) and long reads (>100bp) mappings; It also showed higher sensitivity towards mapping a complex genome like Plasmodium falciparum. The percentage of properly paired reads aligned by NovoAlign, BWA and Stampy were markedly higher. None of the aligners outperforms the others in the benchmark, however the aligners perform differently with genome characteristics. We expect that the results from this study will be useful for the end user to choose aligner, thus enhance the accuracy of read mapping.
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden.
authors.forename: Subazini
authors.initials: S
authors.lastname: Thankaswamy-Kosalai
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden.
authors.forename: Partho
authors.initials: P
authors.lastname: Sen
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden; Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA. Electronic address: intawat@chalmers.se.
authors.forename: Intawat
authors.initials: I
authors.lastname: Nookaew
mesh_terms: D001419:Bacteria / Q000235:genetics; D056890:Eukaryota / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D020080:Tandem Repeat Sequences
keywords: Algorithm; Aligners; Alignments; Genome; Mapping; NGS; Next-generation sequencing; Reads