Introduction¶

pycyseq is a Python library for reading, parsing, and analyzing CySeq sequencing data.

CySeq data is organized according to the SAM format specification and stored in the standard .sam or .bam file format.

CySeq files contain read alignments derived from both single-strand DNA (ssDNA) and double-strand DNA (dsDNA). In addition to the alignment information, CySeq reads derived from dsDNA encode strand-specific mutations and overhang type and length information.

pycyseq is built on top of pysam. It provides a high-level interface for working with CySeq data, making it easy to read and parse alignments, and extract a variety of molecular features from every CySeq read. When lower-level control is required, the underlying pysam API remains fully accessible.