pybwa

Date:

Mar 27, 2026

Version:

2.3.0

Documentation Contents

• Installation
  • Primary Development Commands
  • Shortcut Task Commands
  • For Running Individual Checks
  • For Running All Checks
  • For Running Individual Fixes
  • For Running All Fixes
  • For Running All Fixes and Checks
  • Creating a Release on PyPi
• Introduction
• Examples
  • Align short reads (bwa aln)
  • Align reads (bwa mem)
  • Customize alignment options
  • Reuse an index across multiple alignments
  • Parse alternative hits from the XA tag
  • Control BWA verbosity
  • Use long-read presets (PacBio/ONT)
  • API versus Command-line Differences
• API
  • Bwa Aln
  • Bwa Mem
  • Bwa Index
  • Verbosity