Semblans

Semblans streamlines the automated assembly and processing of RNA-seq data, producing high-quality transcriptome assemblies by abstracting key quality control, reconstitution, and postprocessing steps from raw short-read sequences to annotated coding sequences.

Key Features:

• Automated Quality Control: Semblans abstracts error correction, adapter trimming, and chimera filtration steps required for transcriptome assembly.
• End-to-End Processing: Semblans handles the complete workflow from raw short-read sequences through reconstitution to annotated coding sequences without manual reformatting or restructuring between programs.
• Consistent Assembly Quality: Semblans produced higher quality assemblies for 98 of 101 short-read runs tested when evaluated against previously assembled transcriptomes.

Scientific Applications:

• De Novo Transcriptome Assembly: Semblans assembles transcriptomes from publicly available short-read RNA-seq data using established best practices.
• Comparative Assembly Evaluation: Semblans enables systematic comparison of assembly quality across multiple RNA-seq datasets.

Methodology:

Semblans is written in C++ and implements automated quality control, reconstitution, and postprocessing steps for transcriptome assembly from raw short-read sequences.