Abhimanyu Singh
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TRITEX sequence assembly pipeline for Triticeae genomes
By Jit 2058 days agotritexassembly.bitbucket.io - The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable...Kevler: Reference-free variant discovery in large eukaryotic genomes
By Jit 1897 days agogithub.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
By Jit 1786 days agogithub.com - Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...Published a dataset of 363 genomes from approximately 92 percent of bird families
By Jit 1601 days agoA research team published a dataset of 363 genomes from approximately 92 percent of bird families and showed the significance of sampling dense organisms for biodiversity research.Proksee: in-depth characterization and visualization of bacterial genomes
By LEGE 700 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 53 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)...chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
By Jit 1842 days agogithub.com - Python package to detect chromatin loops (and other patterns) in Hi-C contact maps. Stable version with pip: pip3 install --user chromosight Stable version with conda: conda install -c bioconda -c conda-forge chromosight or, if you want...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 1855 days agogithub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo:...InfoGenomeR: Integrative reconstruction of cancer genome karyotypes
By Jit 1435 days agogithub.com - InfoGenomeR is the Integrative Framework for Genome Reconstruction that uses a breakpoint graph to model the connectivity among genomic segments at the genome-wide scale. InfoGenomeR integrates cancer purity and ploidy, total CNAs, allele-specific...MGRA: Breakpoint graphs and ancestral genome reconstructions
By Jit 2814 days ago Comments (1)http://mgra.cblab.org/ - MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes. It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and...
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