SeqMonk

SeqMonk is a Java-based software application that facilitates a user-friendly environment to help you view and analyze mapped sequence data.

Provided that you have Java installed on your computer, you don't need to set up anything else. This means that you can save the program files in any part of the disk and just click the .jar file to to launch SeqMonk. Otherwise, you can save it to a pen drive to directly run it on any PC with minimum effort. Unlike most installers, it doesn't modify Windows registry settings.

In order to work with SeqMonk, you have to configure a temporary cache directory. Optionally, you can indicate a custom genomes folder too.

It's possible to either browse a list with numerous genomes and download any ones to import into your project, or build one from scratch by specifying various details, such as species, assembly, and number of pseudo-chromosomes.

Apart from viewing and analyzing the genomes graphical representation, SeqMonk lets you explore various information, such as data sets and groups, replicate sets, together with probe lists. You can import data from a wide range of formats, such as text (generic), BAM/SAM, Bed, Bismark, Bowtie, Eland, or GFF. Likewise, you can import annotations.

The current view can be exported to file (chromosome, genome, BEDGraph). It's also possible to copy the current position, select the annotation tracks to display, find a feature, show all labels in the project, set the data zoom level, indicate feature types of ignore, compress the output to reduce its size, and so on.

We haven't come across any stability issues in our tests, thanks to the fact that SeqMonk didn't freeze, crash or display error messages. Its impact on the overall performance of the computer was minimal, since it needed low CPU and RAM to work properly.

Although it doesn't integrate intuitive options for less experienced users, SeqMonk delivers a powerful solution for viewing and analyzing mapped sequence data for experts.