PCI Genomics

158

Title

CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomesuse asterix (*) to get italics

Authors

Julie Orjuela, Aurore Comte, Sébastien Ravel, Florian Charriat, Tram Vi, Francois Sabot, Sébastien CunnacPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year

2022

Picture

Abstract

<p style="text-align: justify;">Using long reads provides higher contiguity and better genome assemblies. However, producing such high quality sequences from raw reads requires to chain a growing set of tools, and determining the best workflow is a complex task. To tackle this challenge, we developed CulebrONT, an open-source, scalable, modular and traceable Snakemake pipeline for assembling long reads data. CulebrONT enables to perform tests on multiple samples and multiple long reads assemblers in parallel, and can optionally perform, downstream circularization and polishing. It further provides a range of assembly quality metrics summarized in a final user-friendly report. CulebrONT alleviates the difficulties of assembly pipelines development, and allow users to identify the best assembly options.</p> <p> </p>

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Keywords

long reads, assemblies, nanopore, pacbio, quality control, snakemake, FAIR, reproducibility

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields

Bioinformatics

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Submission date

2022-02-22 16:21:25

Recommender

Raúl Castanera

Reviewers

Valentine Murigneux

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