Newbler

Newbler performs de novo assembly, reference mapping, and amplicon variant analysis of sequencing reads produced by 454 GS FLX and GS Junior platforms.

Key Features:

• De Novo Assembly: Assembles 454 sequencing reads into contiguous sequences (contigs) for genome assembly.
• Reference Mapping: Maps sequencing reads to reference genomes to support variant detection and comparative analyses.
• Amplicon Variant Analysis: Analyzes genetic variation within PCR-amplified target regions (amplicons) for variant calling.

Scientific Applications:

• Genome Assembly: Reconstruction of genomes from 454 GS FLX and GS Junior read data, including applications such as the Atlantic cod genome assembly.
• Variant Detection: Identification of sequence variants via mapping reads to reference genomes.
• Amplicon Analysis: Targeted analysis of genetic variation within PCR-amplified regions.
• Benchmarking and Evaluation: Performance assessment in assembly competitions and evaluations, e.g., Assemblathon2.

Methodology:

Performs de novo assembly of reads into contigs, maps reads to reference genomes for variant detection and comparative genomics, and conducts targeted amplicon variant analysis.