ALLPATHS

ALLPATHS assembles de novo whole-genome shotgun short reads into contigs, scaffolds, and graph-form assemblies to reconstruct genomes and represent polymorphisms and assembly ambiguities.

Key Features:

• De Novo Assembly: Assembles whole-genome shotgun microreads into contiguous sequences (contigs) and scaffolds from very short reads typical of next-generation platforms such as Illumina-Solexa.
• High-Quality Assemblies: Produces high-coverage assemblies, with demonstrated optimal results at 80x coverage using paired 30-base simulated reads.
• Graph-Based Representation: Outputs assemblies as graphs that retain intrinsic ambiguities, including polymorphisms and alternative reconstructions that linear assemblies may omit.
• Versatility Across Genomes: Applies to genomes from small bacterial species (e.g., Campylobacter jejuni and Escherichia coli yielding single perfect contigs) to larger genomes producing highly connected and accurate assemblies.
• Paired-End Read Integration: Integrates paired-end read information to increase contiguity and assembly accuracy.
• Applicability to Conventional Reads: Implements a general assembly method that can be applied to both short-read and conventional sequence data.

Scientific Applications:

• Microbial Genomics: Reconstruction of bacterial genomes, exemplified by single perfect contig assemblies for Campylobacter jejuni and Escherichia coli.
• Complex Genome Assembly: Assembly of larger and more complex genomes into highly connected and accurate scaffolds and graphs.
• Polymorphism Analysis: Identification and representation of polymorphisms and assembly ambiguities via graph-based outputs for studies of genetic variation and evolution.

Methodology:

Employs a theoretical assembly framework that assembles whole-genome shotgun microreads, integrates paired-end read information to improve contiguity and accuracy, and produces graph-based assembly outputs; the method is applicable to short reads (e.g., Illumina-Solexa) and conventional sequence reads.