SeqMonk

SeqMonk is a cool Java-based software tool that makes it super easy to view and analyze mapped sequence data. If you’ve got Java installed on your computer, you’re all set! You don’t need to go through any complicated setup. Just save the program files anywhere on your disk, and then click the .jar file to launch SeqMonk. Want to take it on the go? You can even save it to a pen drive and run it on any PC without breaking a sweat. Plus, unlike most installers, it doesn’t mess with your Windows registry settings.

Setting Up Your Workspace

To get started with SeqMonk, you will need to set up a temporary cache directory. If you want, you can also point it to a custom genomes folder.

Importing Genomes Easily

You can either browse through a list of numerous genomes and download the ones you need for your project or create one from scratch! Just specify details like species, assembly, and how many pseudo-chromosomes you want.

Exploring Your Data

Besides just viewing and analyzing genomes graphically, SeqMonk allows you to dig into various info such as data sets, groups, replicate sets, and probe lists. You can import data from a bunch of formats like text (generic), BAM/SAM, Bed, Bismark, Bowtie, Eland, or GFF. It also lets you import annotations easily!

Exporting Your Views

Your current view can be exported into different file types like chromosome files or BEDGraph formats. You have options like copying the current position or selecting which annotation tracks to display. Need to find a feature? No problem! You can show all labels in your project and even adjust the data zoom level.

Smooth Performance

No worries about stability issues here! Our tests showed that SeqMonk didn’t freeze or crash at all—it ran smoothly without throwing error messages our way. It’s pretty light on CPU and RAM too, so it won’t slow down your computer while you're working.

A Tool for Experts

While SeqMonk might not have all the intuitive options for beginners out there, it's definitely a powerful tool for experts who want to dive deep into viewing and analyzing mapped sequence data.

If you're interested in trying out SeqMonk for yourself, download here!