sam2lca
dev
Contents:
sam2lca
Python API
Command Line Interface
Databases
Output
Tutorial
Contributing
sam2lca
»
Welcome to sam2lca’s documentation!
Edit on GitHub
Welcome to sam2lca’s documentation!
¶
Homepage:
github.com/maxibor/sam2lca
Contents:
sam2lca
TLDR
Installation
Documentation
Python API
Command Line Interface
sam2lca
Databases
Taxonomy databases
ncbi
gtdb
custom
acc2tax -
accession to TAXID
databases
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
Clone the sam2lca repository, and checkout the dev branch
Install and activate the development environment
Install sam2lca with pip in editable mode
Run the unit and integration tests
Build the documentation
Indices and tables
¶
Index
Module Index
Search Page
Read the Docs
v: dev
Versions
latest
stable
dev
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds