Welcome to sam2lca’s documentation!

Homepage: github.com/maxibor/sam2lca

Contents:

• sam2lca
  • TLDR
  • Installation
  • Documentation
  • Cite
• Python API
• Command Line Interface
  • sam2lca
• Databases
  • Taxonomy databases
  • ncbi
  • gtdb
  • custom
  • acc2tax - accession to TAXID databases
  • Working offline
• Output
  • JSON
  • CSV
  • BAM
  • BAM split by TAXID at given rank
• Tutorial
  • Installing all tools for this tutorial
  • Getting the reference database
  • Indexing the database with Bowtie2
  • Preparing fastq sequencing files
  • Alignment with Bowtie2
  • Optional but (highly) recommended: bamAlignCleaner
  • Running sam2lca
• Contributing
  • 1. Clone the sam2lca repository, and checkout the dev branch
  • 2. Install and activate the sam2lca conda environment
  • 3. Install sam2lca with pip in editable mode
  • Run the unit and integration tests
  • Build the documentation

Indices and tables

• Index

• Module Index

• Search Page