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kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 3227 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...Digest: In silico restriction digest of complete genomes
By Jit 3070 days agoinsilico.ehu.es - This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated. A tool for...mmgenome: Tools for extracting individual genomes from metagneomes
By Jit 2983 days agogithub.com - The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the multi-metagenome concept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole...ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
By BioStar 2850 days agogithub.com - The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2352 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...IRscope: an online program to visualize the junction sites of chloroplast genomes
By Neel 2144 days agosites.google.com - eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust...Proksee: in-depth characterization and visualization of bacterial genomes
By LEGE 1249 days agohttps://proksee.ca/ - Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 2033 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...
