SeqMonk - A Mapped Sequence Analysis tool
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SeqMonk is a tool for viewing and analysing mapped sequence data. It
was initially written to cope with remapping experiment data from
next generation sequencers, but could be applied to any dataset
consisting of a series of mapped genomic regions. The program allows
you to visualise the positions of your mapped regions against an
annotated genome and to quantify the data in order to make comparisons
between data sets.

If you have any comments about SeqMonk the authors would like to hear
them. You either enter them in the bug tracking system at:

https://github.com/s-andrews/seqmonk/issues/

NOTE: this comes with its own JAVA environment.