clc_mapper

clc_mapper maps sequencing reads to reference sequences and assembles them into transcriptome contigs to support analysis of high-throughput sequencing data such as Roche 454 pyrosequencing.

Key Features:

• Read mapping and assembly: Maps short sequencing reads (250-450 base pairs) from Roche 454 pyrosequencing onto reference sequences and assembles them into contigs representing transcripts.
• High-throughput data handling: Processes and analyzes high-throughput sequencing datasets for transcriptome reconstruction.
• Comparative evaluation: Has been systematically compared with assemblers CAP3, MIRA, Newbler, and SeqMan to evaluate assembly performance.
• Assembly merging: Merges assemblies from different programs to improve alignment accuracy with reference sequences and to increase consistency in contig number and size.
• Integration with CLC Genomics Workbench: Operates as part of the CLC Genomics Workbench suite.

Scientific Applications:

• Transcriptome assembly for non-model organisms: Enables assembly and identification of known and novel transcripts where reference genomes are limited or absent.
• Biomedical sequencing analysis: Supports analysis of large next-generation sequencing datasets by producing longer contigs and aligning them to reference sequences.
• Assembler evaluation and optimization: Facilitates evaluation and optimization of assembler combinations and merging strategies to improve final assembly credibility.

Methodology:

Computational methods explicitly include mapping reads to reference sequences, assembling reads into contigs, merging assemblies from different programs, and systematic comparisons with other assemblers.