ABySS

ABySS assembles de novo genomes from short-read sequencing data to produce draft and scaffolded assemblies for genomic variation analysis and reference genome construction.

Key Features:

• Parallelized Assembly: Leverages parallel computing with a message-passing interface (MPI) and evolved algorithms to distribute work and reduce memory requirements for assembling large short-read datasets.
• Probabilistic Data Structures: Represents de Bruijn graphs using Bloom filters to minimize memory footprint during assembly.
• Memory Efficiency and Performance: ABySS 2.0 can achieve a scaffold NG50 of 3.5 Mbp using less than 35 GB of RAM.
• Integration with Long-Read Technologies: Incorporates long-range data from BioNano Genomics and 10x Genomics' Chromium to improve scaffold contiguity, reaching NG50 up to 42 Mbp.

Scientific Applications:

• Genomic Variation Analysis: Provides assembled sequences that enable detailed analysis of genomic variation between species and within individuals.
• Reference Genome Construction: Generates high-quality draft genomes suitable for constructing reference assemblies for comparative genomics.
• Discovery of Novel Sequences: Identifies polymorphic and novel sequences absent from existing human reference assemblies.

Methodology:

Builds and traverses de Bruijn graphs represented with Bloom filters and performs parallelized assembly using MPI and memory-reducing algorithms.