Next-Generation Sequencing Data Analysis, 2nd Edition

Next-Generation Sequencing Data Analysis370

increase in read length. For example, SPAdes, originally developed for de

novo assembly of Illumina short reads [15], has been revised to enable use

of both short and long but less accurate PacBio and ONT reads to achieve

hybrid assembly [16]. New long- read de novo genome assemblers, such as

miniasm [17], Flye [18], NECAT [19], and Raven [20], have been developed

more recently. To accommodate mapping of long reads to a reference genome,

BWA- MEM was a rst attempt to align long reads with the widely used BWA

algorithm. With ultra- long but noisier reads becoming more common, add-

itional aligners, such ...