diff --git a/README.md b/README.md index b734c49..8e185c2 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@

pyCoverM

-pyCoverM is a Python library that provides a simple interface to [CoverM](https://github.com/wwood/CoverM) for fast coverage estimation. +pyCoverM is a Python library that provides bindings to [CoverM](https://github.com/wwood/CoverM), enabling fast coverage estimation. ## Installation -pyCoverM is available through PyPI or Conda. +pyCoverM is available via PyPI or Conda. ### PyPI installation @@ -28,12 +28,13 @@ mamba create -n pycoverm_env -c conda-forge -c bioconda pycoverm mamba activate pycoverm_env ``` -### Quick start +## Quick start pyCoverM provides two functions: -1. `is_bam_sorted` - Verifies if a BAM file is sorted by coordinate. -2. `get_coverages_from_bam` - Computes average contig coverages from sorted BAM files. +1. `is_bam_sorted`: Checks if a BAM file is sorted by coordinate and returns `True` if sorted, or `False` otherwise. +2. `get_coverages_from_bam`: Computes the average contig coverage from sorted BAM files. It returns a tuple where the first element is a list of contig names, and the second is a NumPy array of coverage values. +### Example usage ```py >>> import pycoverm