Table 7 Comparison of main features with other tools for quality assessment of de novo assembly
From: SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies
Feature\Tools | SQUAT | QUAST | REAPR | BUSCO |
|---|---|---|---|---|
Categorization of read-to-assembly mapping relationship | √ | |||
Distributions of alignment scores, mismatch ratios, and clip ratios of read mapping results | √ | |||
Evaluation of assembly quality by identification of poorly/properly mapped reads of different types | √ | |||
Comprehensive metrics for evaluating assembly contiguity. Nx-like plots and cumulative plots | √ | |||
Comparison of multiple assemblies | √ | |||
Identification of scaffolding error by fragment coverage distribution | √ | |||
Evaluation of assembly completeness by single-copy orthologues | √ | |||
Built-in light-weight assessment of read quality by categorizing reads into poor−/medium−/high- quality groups | √ |