HISEA: HIerarchical SEed Aligner for PacBio data.

Background: The next generation sequencing (NGS) techniques have been around for over a decade. Many of their fundamental applications rely on the ability to compute good genome assemblies. As the technology evolves, the assembly algorithms and tools have to continuously adjust and improve.

LASER: Large genome ASsembly EvaluatoR.

Background: Genome assembly is a fundamental problem with multiple applications. Current technological limitations do not allow assembling of entire genomes and many programs have been designed to produce longer and more reliable contigs. Assessing the quality of these assemblies and comparing those produced by different tools is essential in choosing the best ones.

E-MEM: efficient computation of maximal exact matches for very large genomes.

Motivation: Alignment of similar whole genomes is often performed using anchors given by the maximal exact matches (MEMs) between their sequences. In spite of significant amount of research on this problem, the computation of MEMs for large genomes remains a challenging problem. The leading current algorithms employ full text indexes, the sparse suffix array giving the best results.