#39 · Tools & infrastructure
New tools and resources reconcile genome comparison and repeat annotation across…
The dominant thread is infrastructure for comparing genomic sequence and annotation across assemblies, pangenomes, and repeat catalogs. PanMAN, a lossless mutation-annotated network format for pangenomes, reports 3.5-1,391x compression over variation-preserving formats. A comparative analysis of DFAM, HERVd, and RepBase HERV annotations finds major discrepancies in counts and coverage, with up to 93% of records reconciling across resources. ChromoMapper parses QUAST and alignment outputs to visualize collinearity, inconsistencies, and repeats between genome assemblies. Together these works address representation, reconciliation, and visualization of cross-genome differences. The HERV study audits existing resources rather than introducing software, whereas PanMAN and ChromoMapper are new tools.
Published papers
Compressive pangenomics using mutation-annotated networks.
PanMAN, a lossless mutation-annotated network format for pangenomes, achieves 3.5-1,391x compression over variation-preserving formats and encodes evolutionary…
Current status of human endogenous retrovirus annotation.
Comparative analysis of DFAM, HERVd, and RepBase HERV annotations finds major discrepancies in counts and coverage; up to 93% of records reconcile across…
ChromoMapper: a new tool to quickly compare large genome assemblies.
ChromoMapper is a tool that parses QUAST and alignment outputs to visualize collinearity, inconsistencies, and repeats between compared genome assemblies.
Topic history
| Date | Rank |
|---|---|
| #39 |