# 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction

## TL;DR

This paper introduces 2Pipe, a web tool that helps researchers choose the best pipeline for reconstructing microbial genomes from environmental DNA data.

## Contribution

The novel contribution is the development of 2Pipe, an interactive decision-support tool for selecting MAG reconstruction pipelines.

## Key findings

- 2Pipe assists users in selecting suitable MAG reconstruction pipelines based on input data and computational constraints.
- The paper provides a technical overview of 41 publicly available MAG reconstruction pipelines.
- The tool includes a pipeline comparison and a mechanism for developers to add new workflows.

## Abstract

Whole-genome sequencing has boosted our ability to explore microbial
diversity by enabling the recovery of metagenome-assembled genomes (MAGs)
directly from environmental DNA. As a result, the vast availability of
sequencing data has prompted the development of numerous bioinformatics
pipelines for MAG reconstruction, along with challenges to identify the most
suitable pipeline to perform the analysis according to the user needs. This
report briefly discusses the computational requirements of these pipelines;
presents the variety of interfaces, workflow managers, and package managers
they feature; and describes the typical modular structure. Also, it provides
a compacted technical overview of 41 publicly available pipelines or
platforms to build MAGs starting from short and/or long sequences. Moreover,
recognizing the overwhelming number of factors to consider when selecting an
appropriate pipeline, we introduce an interactive decision-support web
application, 2Pipe, that helps users to identify a suitable workflow based
on their input data characteristics, desired outcomes, and computational
constraints. The tool presents a question-driven interface to customize the
recommendation, a pipeline gallery to offer a summarized description, and a
pipeline comparison based on key factors used for the questionnaire. Beyond
this and foreseeing the release of novel pipelines in the near future, we
include a quick form and detailed instructions for developers to append
their workflow in the application. Altogether, this review and the
application equip the researchers with a general outlook of the growing
metagenomics pipeline landscape and guide the users toward deciding the
workflow that best fits their expectations and infrastructure.