二代测序数据分析软件包大全.docVIP

二代测序数据分析软件包大全Integrated solutions*?CLCbio Genomics Workbench?-?de novo?and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Windows, Mac OS X and Linux.*?Galaxy?- Galaxy = interactive and reproducible genomics. A job webportal.*?Genomatix?- Integrated Solutions for Next Generation Sequencing data analysis.*?JMP Genomics?- Next gen visualization and statistics tool from SAS. They are?working with NCGR?to refine this tool and produce others.*?NextGENe?-?de novo?and reference assembly of Illumina, SOLiD and Roche FLX data. Uses a novel Condensation Assembly Tool approach where reads are joined via anchors into mini-contigs before assembly. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Win or MacOS.*?SeqMan Genome Analyser?- Software for Next Generation sequence assembly of Illumina, Roche FLX and Sanger data integrating with Lasergene Sequence Analysis software for additional analysis and visualization capabilities. Can use a hybrid templated/de novo approach. Commercial. Win or Mac OS X.*?SHORE?- SHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. A suite created by the 1001 Genomes project. Source for POSIX.*?SlimSearch?- Fledgling commercial product.Align/Assemble to a reference*?BFAST?- Blat-like Fast Accurate Search Tool. Written by Nils Homer, Stanley F. Nelson and Barry Merriman at UCLA.*?Bowtie?- Ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Transformed (BWT) index.?Link to discussion thread here. Written by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X.*?BWA?- Heng Lees BWT Alignment