TandemTools

TandemTools evaluates and improves assemblies of extra-long tandem repeats (ETRs) in eukaryotic genomes to enable accurate analysis of repetitive regions involved in processes such as chromosome segregation.

Key Features:

• TandemMapper: Maps error-prone reads onto ETRs to produce accurate alignments within highly repetitive regions.
• TandemQUAST: Performs quality assessment of ETR assemblies to identify assembly errors and guide improvements.
• Error identification and correction: Detects and corrects sequencing- and assembly-derived errors in draft ETR assemblies.
• Integration of mapping and QA: Combines read mapping and assembly-quality assessment specifically for extra-long tandem repeats.
• ETR and centromere focus: Targets extra-long tandem repeats in eukaryotic genomes, including centromeric repeats.
• Applicability to long-read assemblies: Operates on ETR assemblies produced with long-read sequencing technologies.

Scientific Applications:

• ETR assembly evaluation: Assess the accuracy and completeness of extra-long tandem repeat assemblies.
• Draft assembly refinement: Refine and correct draft ETR assemblies by leveraging mapped reads and QC metrics.
• Centromere assembly improvement: Improve and validate human centromere assemblies by revealing and rectifying errors.
• Biological analysis of repeats: Support analysis of ETRs implicated in chromosome segregation and other centromere-associated functions.

Methodology:

Composed of two components: TandemMapper for mapping error-prone reads onto ETRs, and TandemQUAST for evaluating assemblies, identifying assembly errors, and improving ETR assemblies.