sam2lca
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Contents:

  • sam2lca
  • Python API
  • Command Line Interface
  • Databases
  • Output
  • Tutorial
  • Contributing
sam2lca
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  • Welcome to sam2lca’s documentation!
  • Edit on GitHub

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
  • 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

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© Copyright 2020, Maxime Borry. Revision 48af5e5e.

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