ngsutilsj is an updated java port of the NGSUtils toolkit. This new version is largely a Java port of the the most commonly used tools from NGSUtils, with some additions thrown in. It is also a library, with utility classes for use in other various NGS related software (such as cgsplice).
Java was chosen for the ease of installation and relative speed (in comparison to the Python NGSUtils). The processing speed for gzipped compressed files was a major reason for the new update.
ngsutilsj is distributed as a self-executing fat-JAR file. This means that for installation, all one needs is
a working copy of Java and the
ngsutilsj file. Unlike other JAR-file based NGS packages, ngsutilsj includes a
shell script shim to make it executable like a traditional Unix program.