SeqMan NGen

SeqMan NGen performs sequence assembly and downstream analysis of traditional and next-generation sequencing data for tasks including variant discovery, coverage evaluation, and consensus annotation.

Key Features:

• Versatile assembly algorithms: Supports multiple assembly algorithms for diverse sequencing data, including next-generation platforms such as Roche 454 pyrosequencing.
• Variant discovery and consensus annotation: Provides functionality for identifying genetic variants and generating consensus annotations from assembled sequences.
• Coverage evaluation: Offers tools to assess sequencing coverage across assemblies to evaluate completeness and depth.
• Optimized transcriptome assembly: Capable of assembling transcriptome data from non-model organisms, exemplified by studies on Litomosoides sigmodontis.
• Integration with Lasergene: Integrates with the Lasergene suite to enable downstream analysis within that software environment.
• Multiple-assembler merging: Supports integration and merging of outputs from multiple assemblers to enhance alignment accuracy and consistency in contig size and number.

Scientific Applications:

• Transcriptome analysis: Generation and analysis of transcriptomes from complex or less-studied organisms.
• Variant discovery and annotation: Identification and annotation of genetic variants for studies of genomic diversity and function.
• Coverage assessment: Evaluation of sequencing coverage to inform assembly quality and completeness.
• Assembly consolidation: Combining outputs from different assembly programs to produce a more credible final assembly for downstream analyses.

Methodology:

SeqMan NGen leverages different assembly algorithms and can integrate and merge outputs from multiple assemblers; in comparative studies it has recapitulated known transcripts and generated novel sequences but can produce an excess of small, redundant contigs.