A5-miseq

A5-miseq performs de novo assembly of Illumina MiSeq paired-end reads to generate contigs and scaffolds for microbial genome analysis.

Key Features:

• Automated workflow: Automates adapter trimming, quality filtering, error correction, and contig and scaffold generation for de novo assembly.
• Enhanced read handling: Utilizes Illumina MiSeq long reads and paired-end read information during contig generation to improve assembly completeness and recovery of reference genes.
• Adapter trimming: Removes sequencing adapters from raw reads to prevent interference in downstream assembly.
• Quality filtering: Filters reads by quality to ensure high-quality input for assembly.
• Error correction: Performs read error correction prior to assembly to reduce incorporation of sequencing errors into contigs.
• Contig and scaffold generation: Constructs contiguous sequences and scaffolds using paired reads to represent genomic architecture.
• Misassembly detection: Detects potential misassemblies using internal algorithms to improve assembly fidelity.
• Data submission support: Provides scripts to facilitate submission of assemblies to NCBI and integration with the RAST annotation system.

Scientific Applications:

• Bacterial and microbial genome assembly: Assembles bacterial and other microbial genomes from Illumina MiSeq sequence data.
• Recovery of reference genes: Produces assemblies that support recovery of complete gene sets for downstream analyses.
• Comparative genomics: Enables comparative genomics by providing assembled genomes for genome-to-genome comparisons.
• Functional annotation: Supports functional annotation workflows, including integration with RAST, using assembled sequences.
• Evolutionary studies: Facilitates evolutionary and phylogenetic analyses by supplying assembled genomic data.

Methodology:

Adapter trimming, quality filtering, error correction, contig and scaffold generation using paired-end and MiSeq long-read information, misassembly detection, and scripts for NCBI submission and RAST integration.