apscale-nanopore 1.0.1

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Nanopore application

apscale

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

- apscale

- apscale_blast

apscale-nanopore

Introduction

Apscale-nanopore is a modified version of the metabarcoding pipeline apscale and is used for the processing of Oxford Nanopore data.

Programs used:

• cutadapt
• vsearch
• swarm
• blast+ (blastn module)

Input:

• Non-demultiplexed Nanopore sequence data in .fastq format.

Output:

• read table, taxonomy table, log files

Installation

Apscale-nanopore can be installed on all common operating systems (Windows, Linux, MacOS). Apscale-nanopore requires Python 3.10 or higher and can be easily installed via pip in any command line:

pip install apscale_nanopore

To update apscale-blast run:

pip install --upgrade apscale_nanopore

The easiest installation option is the Conda apscale environment. This way, all dependencies will automatically be installed.