Arachne

Arachne assembles genome sequences from paired-end whole-genome shotgun sequencing data to reconstruct genomes and resolve repeats.

Key Features:

• Efficient Read Overlap Detection: Arachne employs an efficient and sensitive procedure to identify overlaps between reads.
• Error Correction and Scoring: It scores read overlaps to correct errors and improve assembly accuracy prior to final assembly.
• Read Merger via Forward-Reverse Links: The tool utilizes forward-reverse linkages to merge reads and reconstruct original sequence across complex regions.
• Repeat Contig Detection: Arachne detects repeat contigs by identifying inconsistencies in forward-reverse links.
• Contig Joining and Scaffolding: The software joins contigs into supercontigs or scaffolds to minimize the number of contigs.

Scientific Applications:

• Benchmark Genomes: Assemblies have been generated from simulated reads (~10-fold coverage) for Haemophilus influenzae, Saccharomyces cerevisiae, Drosophila melanogaster, and human chromosomes 21 and 22.
• Drosophila assembly metrics: On Drosophila melanogaster Arachne achieved approximately 98% genome coverage with an N50 contig length of 324 kb and an N50 supercontig length of 5143 kb, with small errors (~1 per 1 Mb) typically involving ~1 kb deletions.
• Computational performance: The Drosophila genome assembly completed in 21 hours on a single 667 MHz processor using 8.4 GB of memory.
• Research domains: Results support applications in de novo genome assembly, comparative genomics, evolutionary biology, and medical genetics.

Methodology:

Assemblies were created from simulated reads at approximately 10-fold coverage; methods explicitly include sensitive read-overlap detection, scoring-based error correction of overlaps, merging via forward-reverse links, detection of repeat contigs from link inconsistencies, and joining contigs into supercontigs or scaffolds with performance evaluated by genome coverage and contig reduction.