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GIGGLE: a search engine for large-scale integrated genome analysis
By Jit 2540 days agogithub.com - GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is...Carrot2 clustering engine
By LEGE 627 days agosearch.carrot2.org - This is the demo application of the Carrot2 clustering engine. It uses Carrot2's algorithms to organize search results into thematic folders. User interfaces Web Search Clustering organizes search results from public...Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
By Jit 3164 days agobioinformatics.ua.pt - Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For...Spines
By Jit 2948 days agowww.broadinstitute.org - Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation...J-Circos
By Shruti Paniwala 2867 days agowww.australianprostatecentre.org - Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom...progressiveCactus
By Abhimanyu Singh 2777 days agogithub.com - Progressive Cactus is a whole-genome alignment package. Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules https://github.com/glennhickey/progressiveCactusSIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
By Neel 2588 days agohciweb.iwr.uni-heidelberg.de - This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit,...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2301 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...KAST
By Neel 1035 days agogithub.com - Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 1379 days ago Comments (1)github.com - DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools...
