Jit
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kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2542 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...PGAP-X: Extension on pan-genome analysis pipeline
By Rahul Nayak 2496 days agohttps://pgapx.ybzhao.com/ - PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different...bpRNA: large-scale automated annotation and analysis of RNA secondary structure
By Rahul Nayak 2377 days agogithub.com - bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 1764 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...Juicebox: Visualization and analysis software for Hi-C data
By Jit 1738 days agogithub.com - Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is...wgd—simple command line tools for the analysis of ancient whole-genome duplications
By LEGE 1585 days agogithub.com - wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these...Kmer: a suite of tools for DNA sequence analysis
By BioStar 1194 days agohelp.rc.ufl.edu - More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assembly to Assembly Comparision tool: Comparative mapping between two genome assemblies (same species), or between two different genomes (cross...InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams
By Jit 879 days agowww.interactivenn.net - InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are...pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction
By LEGE 277 days agogithub.com - ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across...NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).
By Poonam Mahapatra 4121 days agoThe 4-day course is organized as a series of morning lectures and afternoon hands-on workshops.
