pathMap: a path-based mapping tool for long noisy reads with high sensitivity.

With the rapid development of single-molecule sequencing (SMS) technologies, the output read length is continuously increasing. Mapping such reads onto a reference genome is one of the most fundamental tasks in sequence analysis. Mapping sensitivity is becoming a major concern since high sensitivity can detect more aligned regions on the reference and obtain more aligned bases, which are useful for downstream analysis.

Comparison of Methods for Biological Sequence Clustering.

Recent advances in sequencing technology have considerably promoted genomics research by providing high-throughput sequencing economically. This great advancement has resulted in a huge amount of sequencing data. Clustering analysis is powerful to study and probe the large-scale sequence data.

kngMap: Sensitive and Fast Mapping Algorithm for Noisy Long Reads Based on the -Mer Neighborhood Graph.

With the rapid development of single molecular sequencing (SMS) technologies such as PacBio single-molecule real-time and Oxford Nanopore sequencing, the output read length is continuously increasing, which has dramatical potentials on cutting-edge genomic applications. Mapping these reads to a reference genome is often the most fundamental and computing-intensive step for downstream analysis. However, these long reads contain higher sequencing errors and could more frequently span the breakpoints of structural variants (SVs) than those of shorter reads, leading to many unaligned reads or reads that are partially aligned for most state-of-the-art mappers.