Allpaths-LG

Allpaths-LG assembles large and complex genomes de novo from Illumina short-read, massively parallel sequencing data to produce accurate and contiguous draft assemblies.

Key Features:

• Algorithmic Innovation: Handles repetitive sequences typical of large mammalian genomes and integrates massively parallel Illumina short-read data for assembly.
• Base Accuracy: Produces assemblies with reported base accuracy ≥99.95%.
• Contiguity: Delivers both short-range contiguity and long-range connectivity in assembled genomes.
• Scaffold Size: Generates large scaffold N50 values (human 11.5 Mb; mouse 7.2 Mb) comparable to those from capillary-based sequencing.
• Genome Coverage: Ensures extensive coverage of target genomes to support comprehensive assembly.

Scientific Applications:

• De Novo Genome Assembly: Constructs draft genome assemblies for large and complex vertebrate genomes from short-read data.
• Comparative Genomics: Provides high-quality assemblies that enable cross-species comparative analyses.
• Genomic Research: Supports gene discovery, functional genomics, and studies of genetic variation.

Methodology:

Employs an advanced algorithm that optimizes assembly of short-read, massively parallel sequencing data and uses computational innovations to manage repetitive sequences and large genome sizes.