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Updated: Dec 23, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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

yacrd and fpa: upstream tools for long-read genome assembly

Pierre Marijon¹, Rayan Chikhi², Jean-Stéphane Varré³

¹Department of Computer Science, Inria, Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL, Lille F-59000, France.

Bioinformatics (Oxford, England)

|April 22, 2020

Abstract

Motivation:

Genome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space.

Results:

We introduce two tools: yacrd for chimera removal and read scrubbing, and fpa for filtering out spurious overlaps. We show that yacrd results in higher-quality assemblies and is one hundred times faster than the best available alternative.

Availability And Implementation:

https://github.com/natir/yacrd and https://github.com/natir/fpa.

Supplementary Information:

Supplementary data are available at Bioinformatics online.

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Related Concept Videos

Genome Annotation and Assembly

Genome 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.

RNA-seq

RNA-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...

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