weeSAM

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usage:

weeSAM { --bam file.bam OR --sam file.sam } --out output.txt

command line options:

--bam : The input bam file. [file.bam]
--sam : The input sam file. [file.sam]
--out : The name of your output file. [myoutput.txt]
--html: Generate html for each coverage plot produced by the script. [file.html]
--overwrite : Add this flag to overwrite a html directory from a previous run. --mapped : Add to generate and analyse a new bam file with only mapped reads. -h : Print help function.
-v : weeSAM version number.

File output fields:

Ref_Name : The identifier of the reference.
Ref_Len : The length in bases of each reference.
Mapped_Reads : Number of reads mapped to each reference.
Breadth : The number of sites in the genome covered by reads.
%_Covered : The percent of sites in the genome which have coverage.
Min_Depth : Minimum read depth observed.
Max_Depth : Max read depth observed.
Avg_Depth : Mean read depth observed.
Std_Dev : Standard deviation of the mean (Avg_Depth).
Above_0.2_Depth : Percentage of sites which have greater than 0.2 * Avg_Depth.
Above_1_Depth : Percentage of sites which are above Avg_Depth.
Above_1.8_Depth : Percentage of sites which have greater than 1.8 * Avg_Depth.
Variation_Coefficient : The mean of Std_Dev of the mean.

Installation

You will need pysam and seaborn to run weeSAM.

For easy installation of these:

pip install pysam

and

pip install seaborn

Then clone the repo:

git clone https://github.com/centre-for-virus-research/weeSAM.git

Then, weeSAM should work by providing the path to the python script, for example from within repo directory e.g:

./weeSAM -h