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.

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Lander-Waterman’s coverage bound establishes the total number of reads required to cover the whole genome of size G bases. In fact, their bound is a direct consequence of the well-known solution to the coupon collector’s problem which proves that for such genome, the total number of bases to be sequenced should be O(G ln G). Although the result leads to a tight bound, it is based on a tacit assumption that the set of reads are first collected through a sequencing process and then are processed through a computation process, i.e., there are two different machines: one for sequencing and one for processing. In this paper, we present a significant improvement compared to Lander-Waterman’s result and prove that by combining the sequencing and computing processes, one can re-sequence the whole genome with as low as O(G) sequenced bases in total. Our approach also dramatically reduces the required computational power for the combined process. Simulation results are performed on real genomes with different sequencing error rates. The results support our theory predicting the log G improvement on coverage bound and corresponding reduction in the total number of bases required to be sequenced.

In CDMA systems, the received user powers vary due to moving distance of users. Thus, the CDMA receivers consist of two stages. The first stage is the power estimator and the second one is a Multi-User Detector (MUD). Conventional methods for estimating the user powers are suitable for underor fully-loaded cases (when the number of users is less than or equal to the spreading gain). These methods fail to work for overloaded CDMA systems because of high interference among the users. Since the bandwidth is becoming more and more valuable, it is worth considering overloaded CDMA systems. In this paper, an optimum user power estimation for over-loaded CDMA systems with Gaussian inputs is proposed. We also introduce a suboptimum method with lower complexity whose performance is very close to the optimum one. We shall show that the proposed methods work for highly over-loaded systems (up to m (m + 1) /2 users for a system with only m chips). The performance of the proposed methods is demonstrated by simulations. In addition, a class of signature sets is proposed that seems to be optimum from a power estimation point of view. Additionally, an iterative estimation for binary input CDMA systems is proposed which works more accurately than the optimal Gaussian input method.