Related Experiment Video
Updated: Jun 26, 2026
12:08
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
LORA: a polymorphic multi-sample long read assembly pipeline
Dimitri Desvillechabrol1,2, Rania Ouazahrou1,2, Juliana Pipoli da Fonseca3
1Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, F-75015 Paris, France.
NAR Genomics and Bioinformatics
|June 25, 2026
Summary
LORA is a new, user-friendly application for genome assembly using long-read sequencing data. It integrates multiple tools and quality checks, ensuring reproducible and high-quality genomic results for diverse species.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Long-read sequencing is crucial for high-contiguity genome assembly, especially for complex genomic regions.
- Existing genome assemblers vary in performance and reproducibility, posing challenges for researchers.
- The need for standardized, reproducible workflows in genome assembly is critical.
Purpose of the Study:
- To develop LORA, an easy-to-use and reproducible application for genome assembly from long-read sequencing data.
- To integrate multiple established and novel genome assembly tools into a single pipeline.
- To provide comprehensive quality assessment and reporting features for genome assemblies.
Main Methods:
- LORA is implemented as a Snakemake pipeline for parallel task execution and cluster compatibility.
- It integrates assemblers such as Canu, HiFiasm, Flye, Unicycler, Necat, and Pecat.
- Includes quality assessment, interactive HTML reports, taxonomic identification (BLAST), and completeness evaluation.
Main Results:
- Demonstrated LORA's capability in assembling bacterial and unicellular eukaryotic genomes using PacBio and Oxford Nanopore data.
- Highlighted typical outcomes and common pitfalls in long-read genome assembly workflows.
- Provided a comprehensive view of assembly quality and potential issues through integrated reporting.
Conclusions:
- LORA offers a reproducible and comprehensive solution for long-read genome assembly.
- The application facilitates the interpretation of assembly quality and identification of potential problems.
- LORA is part of the Sequana project, promoting reproducibility and ease of deployment.
Related Concept Videos
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:35RACE - Rapid Amplification of cDNA Ends
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
Since the...