# What is SeqMonk

SeqMonk is a program for visualising and analysing large set of mapped genomic regions. It was desgined to work with data from high throughput sequencing technologies, but will work just as well with any set of mapped reads.

SeqMonk provides a genome browser which allows you to navigate quickly around an annotated genome and a data browser which puts your sequence reads in their appropriate genomic context. It also includes a set of tools to allow you to quantitate and filter your data so that you can find regions of interest in a systematic way.

## What is SeqMonk useful for?

SeqMonk was designed to be as flexible as possible and should be useful in a wide variety of experimental designs. Types of experiment which are known to have been successfully analysed with SeqMonk are:

- ChIP-Seq
- Chromosome Conformation Capture
- High-throughput Bisulphite Sequencing
- Analysis of genomic deletions/duplications

## What is SeqMonk not useful for?

There are some types of experiment to which SeqMonk is not directly suited. These limitations stem from the fact that SeqMonk deals only in genomic locations - it does not record the sequence underlying each mapped read. This means it is not useful for SNP identification. In these types of experiments though we have pre-processed the data to segregate the WT and mutant sequences into separate datasets and then loaded these into SeqMonk for analysis.

SeqMonk requires an annotated genome against which to work - therefore experiments involving the assembly of novel sequence or those using species without an assembled genome cannot be analysed with SeqMonk. Although we have a wide range of genomes available in SeqMonk you may find that a genome you want to use is not present. In this case please contact the authors who can either add the genome to their standard list, or tell you how to create the necessary files on your system.