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Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.\n\nMaq first aligns reads to reference sequences and then calls the consensus. At the mapping stage, maq performs ungapped alignment. For single-end reads, maq is able to find all hits with up to 2 or 3 mismatches, depending on a command-line option; for paired-end reads, it always finds all paired hits with one of the two reads containing up to 1 mismatch. At the assembling stage, maq calls the consensus based on a statistical model. It calls the base which maximizes the posterior probability and calculates a phred quality at each position along the consensus. Heterozygotes are also called in this process.

Velvet\nSequence assembler for very short reads\n\nCurrent version: 0.7.63\n\nManual in pdf format\n\nPublic Git URL: git clone git://github.com/dzerbino/velvet.git\n\nFor up-to-date info, you can consult and/or subscribe to the mailing list.

Dominating the Next Generation Sequencing data analysis challenge\n\nWe have overcome the challenge to analyze Next Generation Sequencing data faster than it is produced by implementing a SIMD-accelerated assembly algorithm in our Next Generation Sequencing solution, CLC Genomics Workbench - a cross-platform desktop application with a graphical user-interface.\nCLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.