PGcloser

PGcloser closes gaps in draft genome assemblies using long-reads or contigs to improve assembly completeness and accuracy.

Key Features:

• Parallel Processing: Operates in parallel mode to reduce computational time compared to other long-read-based gap-closing tools.
• Long-Read and Contig Utilization: Uses long-reads or contigs instead of short reads from next-generation sequencing to fill gaps and enhance assembly coverage.
• Modular Design: Comprised of seven modules—SplitFa, ExtrGap, BwtBuilt, CompGap, ClsGap, MergFa, and GetCls—for splitting input, extracting gaps, building indices, comparing sequences, closing gaps, merging results, and retrieving outputs.
• Performance: Demonstrated faster runtime than other gap-closing tools while maintaining similar levels of accuracy in comparative tests.

Scientific Applications:

• Genome assembly improvement: Enhances completeness of draft genome assemblies by closing sequence gaps with long-reads or contigs.
• Evolutionary biology: Provides more complete assemblies suitable for evolutionary analyses.
• Functional genomics: Produces more continuous genome sequences that support functional genomic studies.
• Comparative genomics: Improves assembly continuity to facilitate genome-to-genome comparisons.

Methodology:

Pipeline composed of seven modules (SplitFa, ExtrGap, BwtBuilt, CompGap, ClsGap, MergFa, GetCls) that split input FASTA, extract gaps, build indices (BwtBuilt), compare sequences, close gaps, merge results, and retrieve closed sequences.