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Article Dans Une Revue BMC Bioinformatics Année : 2023

MTG-Link: leveraging barcode information from linked-reads to assemble specific loci

Résumé

Background: Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. Results: We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. Conclusions: MTG-Link is an efficient local assembly tool designed for different linkedread sequencing technologies. MTG-Link source code is available at https:// github. com/ anne-gcd/ MTG-Link and as a Bioconda package.
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Origine : Publication financée par une institution
Licence : CC BY - Paternité

Dates et versions

hal-04166273 , version 1 (19-07-2023)

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Paternité

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Anne Guichard, Fabrice Legeai, Denis Tagu, Claire Lemaitre. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci. BMC Bioinformatics, 2023, 24 (1), pp.284. ⟨10.1186/s12859-023-05395-w⟩. ⟨hal-04166273⟩
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