Tigmint

Tigmint corrects misassemblies in genome assembly drafts by using linked and long sequencing reads (e.g., 10x Genomics Chromium) to detect discrepancies between reads and assemblies and improve assembly accuracy and contiguity.

Key Features:

• Linked-read support: Leverages long-distance information from linked reads such as 10x Genomics Chromium to detect assembly inconsistencies.
• Long-read compatibility: Applies to assemblies derived from long single-molecule sequencing as well as short-read assemblies.
• Reference-free misassembly detection: Identifies misassemblies by comparing sequencing data to the assembled sequence without requiring a reference genome.
• Misassembly correction: Locates and corrects predicted misassembly sites to improve local sequence accuracy and downstream scaffolding.
• Scaffolding integration: Can be combined with scaffolding tools such as ARCS to increase scaffold contiguity.
• Assembler compatibility: Demonstrated on assemblies produced by ABySS 2.0 and applicable to other assemblers.
• Quantified improvements: Shown to reduce misassemblies (e.g., 216 fewer misassemblies, a 27% reduction in an ABySS assembly as measured by QUAST) and to increase scaffold NGA50 when combined with ARCS (from 3 Mbp to 16.4 Mbp).

Scientific Applications:

• De novo assembly refinement: Corrects misassemblies in draft genomes assembled from short reads or long reads without a reference genome.
• Scaffolding enhancement: Improves scaffold contiguity when used prior to or in combination with ARCS and linked-read scaffolding.
• Hybrid assembly improvement: Integrates linked reads with long single-molecule sequencing to achieve both high sequence contiguity and high scaffold contiguity.
• Assembly evaluation and benchmarking: Used in demonstrated evaluations of human genome assemblies with QUAST and ABySS 2.0.

Methodology:

Compares sequencing data (linked or long reads, e.g., 10x Genomics Chromium) to assembled sequences to identify discrepancies indicative of misassemblies, applies corrections at predicted misassembly sites, and can be followed by scaffolding with ARCS.