FGAP

FGAP closes gaps in draft genome assemblies by aligning contigs and reads from multiple sequencing technologies to improve assembly completeness and accuracy.

Key Features:

• Multi-Technology Integration: FGAP utilizes data from Illumina, 454 and PacBio sequencing platforms to exploit complementary strengths for gap closure.
• Automated Gap Closure: FGAP identifies and closes gaps by aligning contigs against the draft assembly using BLAST to detect overlapping sequences.
• Optimal Sequence Selection: FGAP selects and inserts the sequence that best bridges each identified gap based on its selection algorithm.
• Validation and Accuracy: FGAP validates inserted sequences against a reference genome using QUAST to assess assembly quality and fidelity.

Scientific Applications:

• Escherichia coli draft assemblies: In an E. coli draft genome, FGAP reduced the number of gaps by 78% when integrating Illumina and 454 data.
• PacBio long-read assemblies: With PacBio long reads, FGAP achieved a 98% gap-closure rate.
• Human chromosome 14 assemblies: FGAP reduced gap counts by 35% in human chromosome 14 assemblies.

Methodology:

FGAP integrates datasets from Illumina, 454 and PacBio, aligns contigs against the draft assembly using BLAST to identify overlapping sequences, selects and inserts optimal sequences to fill gaps, and validates inserted sequences with QUAST against a reference genome.