Jit
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TRITEX sequence assembly pipeline for Triticeae genomes
By Jit 2489 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 2328 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 2217 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 2032 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 1130 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 484 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)...GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome...
By Jit 2815 days agogithub.com - GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps: Step 1. Run mugsy to get multiple sequence alignment results. Step 2 & 3. Extraction of the Coordinates...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 2285 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:...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3120 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...
Run miniasm assembler on nanopore reads !
Last updated 3099 days ago by Jit Comments (5)Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...
