Next Generation Sequencing (NGS) has become an important technique to study genomic differences. Its daily production reaches billions of short reads that need to align with the reference genome in many NGS applications. Dr. Wen-Lian Hsu and his postdoctoral Fellow Dr. Hsin-Nan Lin in the Information Science Institute have recently developed a parallel “approximate alignment” algorithm: KART, which is 3 to 10 times faster than the well-known Bowtie2 and BWA-MEM algorithm. On pairwise alignment of human genome sequences, KART is 200 times faster than current methods. The same idea has also been applied to RNA-seq, producing DART, a quick and accurate mapping algorithm. These two results are published in Bioinformatics and the source codes can be downloaded.

s Kart: a divide-and-conquer algorithm for NGS read alignment:

https://goo.gl/FKNaaq

s DART: a fast and accurate RNA-seq mapper with a partitioning strategy:

https://goo.gl/JFswSj