Deeptools is a python processing suite for bamfiles and renders them into genome browser track forms as such as bed and bigwig.
It can be invoked in three ways, from the command line, using Galaxy or via an API against which you would write python scripts.
Its command-line tools do not work via the subcommand convention but have their own principle command.
$ deeptools -h usage: deeptools [-h] [--version] deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Each tool should be called by its own name as in the following example: $ bamCoverage -b reads.bam -o coverage.bw If you find deepTools useful for your research please cite as: Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. 2016. "deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis." Nucleic Acids Research, April. doi:10.1093/nar/gkw257. [ Tools for BAM and bigWig file processing ] multiBamSummary compute read coverages over bam files. Output used for plotCorrelation or plotPCA multiBigwigSummary extract scores from bigwig files. Output used for plotCorrelation or plotPCA correctGCBias corrects GC bias from bam file. Don't use it with ChIP data bamCoverage computes read coverage per bins or regions bamCompare computes log2 ratio and other operations of read coverage of two samples per bins or regions bigwigCompare computes log2 ratio and other operations from bigwig scores of two samples per bins or regions computeMatrix prepares the data from bigwig scores for plotting with plotHeatmap or plotProfile [ Tools for QC ] plotCorrelation plots heatmaps or scatterplots of data correlation plotPCA plots PCA plotFingerprint plots the distribution of enriched regions bamPEFragmentSize returns the read length and paired-end distance from a bam file computeGCBias computes and plots the GC bias of a sample plotCoverage plots a histogram of read coverage [Heatmaps and summary plots] plotHeatmap plots one or multiple heatmaps of user selected regions over different genomic scores plotProfile plots the average profile of user selected regions over different genomic scores plotEnrichment plots the read/fragment coverage of one or more sets of regions [Miscellaneous] computeMatrixOperations Modifies the output of computeMatrix in a variety of ways. For more information visit: http://deeptools.readthedocs.org optional arguments: -h, --help show this help message and exit --version show program's version number and exit