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Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
By Jit 1791 days agogithub.com - Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2579 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
By Neel 1744 days agogdblab.com - GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction. GSP4PDB is part of the services provided by the Bioinformatic Group of the University of...Carrot2 clustering engine
By LEGE 625 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...RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
By Jit 2583 days agokiwi.cs.dal.ca - RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to...BioCircos.js is an open source interactive Javascript library to interactive display biological...
By Jit 2529 days agobioinfo.ibp.ac.cn - BioCircos.js is an open source interactive Javascript library which provides an easy way to interactive display biological data on the web. It implements a raster-based SVG visualization using the open source Javascript...AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Jit 2369 days ago Comments (1)github.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC...SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
By Jit 2295 days agowww.bioinformatics.babraham.ac.uk - SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic...NanoPack: visualizing and processing long-read sequencing data
By Jit 2189 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish...
By Jit 2162 days agogithub.com - Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless...
