pysequila’s documentation

PySeQuiLa is a Python wrapper for SeQuiLa, an ANSI-SQL compliant solution for distributed processing of Next Generation Sequencing data built on top of Apache Spark. PySeQuiLa extends Apache Spark SQL with highly efficient implementations of common bioinformatics operations such as interval joins, depth of coverage or pileup (see Algorithms and Benchmarks). It combines analytical power of Python with SQL syntax for almost unlimited querying and processing of NGS data.

For any topics not covered here please refer to SeQuiLa documentation

Contents:

• Quick start
• Initialize
• File formats
• Genomic intervals
• Coverage analysis
• Pileup analysis
• Running on GKE (Google Kubernetes Engine)
• Benchmarking
• License and citation