Jit
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HaploTypo: a variant-calling pipeline for phased genomes
By Jit 2481 days agogithub.com - An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve...CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
By Jit 2034 days agogithub.com - The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and thus support the assembly process. This typically results in...IRscope: an online program to visualize the junction sites of chloroplast genomes
By Neel 2138 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 1243 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.TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes
By LEGE 597 days agotritexassembly.bitbucket.io - This is the documentation of TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes. It was developed in the research group Domestication Genomics at the Leibniz Institute of Plant Genetics and Crop Research (IPK)...Metagenomics assembly workshop !!
By Jit 3456 days agodenbi-metagenomics-workshop.readthedocs.io - Welcome to the one-day metagenomics assembly workshop. This tutorial will guide you through the typical steps of metagenome assembly and binning. The Tutorial Data Set FastQC Quality Control Assembly Velvet Assembly MEGAHIT...Omega2: metagenome assembly pipeline
By Jit 3373 days agoomega.omicsbio.org - Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph...Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 1403 days agohttps://github.com/envgen - Useful Metagenomics resourcesITIS: the Integrated Taxonomic Information System!
By Jit 2591 days agohttps://www.itis.gov/ - ITIS, the Integrated Taxonomic Information System! Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. We are a partnership of U.S., Canadian,...Recombination detection tool
By Jit 3897 days ago Comments (2)github.com - A program to detect recombination hotspots using population genetic data. More at https://github.com/auton1/LDhot
