Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter.
To install the stable version:
pip3 install --user tinycov
To install the development version:
git clone https://github.com/cmdoret/tinycov.git
cd tinycov
pip install .
Only a BAM file alignment is required as input. If it is not coordinate-sorted, tinycov will make a sorted copy named input.sorted.bam if the file is named input.bam.
If no output is provided, the coverage plot will be displayed interactively using matplotlib. If --out is used, the plot will be saved in a format determined by the output file's extension.
Additionally, if --text is provided, an output text file will be saved in the bedgraph format with overlapping windows (depending on the values of --res and --skip).
The tinycov commands can be invoked from the command line to list subcommands.
Usage: tinycov [OPTIONS] COMMAND [ARGS]...
tinycov: visualisation of coverage from BAM files using rolling window
averages.
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
covhist Visualise the histogram of coverage in rolling windows.
covplot Visualise coverage in rolling windows, optionally save results
to...
The covplot subcommand plots the coverage in sliding windows along the genome. A bedgraph file with the coverage of each window can be generated using the --text option.
Usage: tinycov covplot [OPTIONS] BAM
Visualise coverage in rolling windows, optionally save results to a
bedgraph file.
Options:
-N, --no-filter Use all reads. By default, PCR duplicates and
secondary alignments are excluded
-m, --max-depth INTEGER Maximum read depth permitted. Position with higher
coverage will set to this value
-o, --out PATH Output file where to write the plot. If not
provided, the plot is shown interactively
-w, --whitelist TEXT Only include those chromosomes in the plot. List of
comma-separated chromosome names.
-b, --blacklist TEXT Exclude those chromosomes from the plot. List of
comma-separated chromosome names.
-n, --name TEXT Name of the sample (plot title). Base name of input
file by default
-B, --bins TEXT Tab-separated file of three columns (chromosome,
start, end) without header containing a custom
binning to use. Overrides --res and --skip,
optional.
-s, --skip INTEGER Stride between windows, in basepairs. [default:
1000]
-r, --res INTEGER Size of windows in which to compute coverage, in
basepairs. [default: 10000]
-t, --text PATH Output file where to write the raw data table.
-p, --ploidy INTEGER Ploidy of input sample, used to estimate coverage
threshold for aneuploidies. Setting to 0 disables
estimations.
--version Show the version and exit.
--help Show this message and exit.
The covhist subcommands generates a histogram of coverage values by window. To get a histogram of coverage by basepair, just set --res to 1.
Usage: tinycov covhist [OPTIONS] BAM
Visualise the histogram of coverage in rolling windows.
Options:
-N, --no-filter Use all reads. By default, PCR duplicates and
secondary alignments are excluded
-m, --max-depth INTEGER Maximum read depth permitted. Position with higher
coverage will set to this value
-o, --out PATH Output file where to write the plot. If not
provided, the plot is shown interactively
-w, --whitelist TEXT Only include those chromosomes in the plot. List of
comma-separated chromosome names.
-b, --blacklist TEXT Exclude those chromosomes from the plot. List of
comma-separated chromosome names.
-n, --name TEXT Name of the sample (plot title). Base name of input
file by default
-B, --bins TEXT Tab-separated file of three columns (chromosome,
start, end) without header containing a custom
binning to use. Overrides --res and --skip,
optional.
-s, --skip INTEGER Stride between windows, in basepairs. [default:
1000]
-r, --res INTEGER Size of windows in which to compute coverage, in
basepairs. [default: 10000]
--version Show the version and exit.
--help Show this message and exit.