Results for "Assembly"

Tags

  • TIGER: tiled iterative genome assembler https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526431/ #genome #assembly #tool

    Tags: genome, assembly, tool

    1916 days ago

  • CANU genome assembly parameters !

    Choose the appropriate parameters to run Canu and run it. The assembly will take about an hour. You can use two cores (parameter -maxThreads=2) and you would like to disable cluster option, since we compute on a single Amazon server set off the option to compute on cluster useGrid=false...

    Tags: CANU, genome, assembly, parameters, NGS, LongReads, OLC

    1907 days ago

  • Long reads assembly tutorial https://www.melbournebioinformatics.org.au/tutorials/tutorials/pacbio/ #Long #Reads #PacBio #assembly #Genome

    Tags: Long, Reads, PacBio, assembly, Genome

    1907 days ago

  • Genome assembly tutorial https://bioinformaticsdotca.github.io/high-throughput_biology_2017_module6_lab #tutorial #assembly #tools #steps #pipeline

    Tags: tutorial, assembly, tools, steps, pipeline

    1895 days ago

  • Genome assembly tutorial "Genome Assembly for short and long reads"

    In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know: How to perform basic quality checks on the...

    Tags: Genome, assembly, tutorial, short, long, reads

    1895 days ago

  • SvABA: Genome-wide detection of structural variants and indels by local assembly

    SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (wi...

    Tags: SvABA, Genome-wide, detection, structural, variants, indels, local, assembly

    1893 days ago

  • List of tools frequently used while genome assembly

    List of tools frequently used while genome assembly: I have used the following assemblers Spades (v. 3.10.1) CANU (v. 1.6) Unicycler (v. v0.4.1) Miniasm (v. 0.2-r137-dirty) I have used the following mappers minimap2 (v. 2.0rc1-r232) minimap (v. 0.2...

    Tags: List, tools, frequently, genome, assembly

    1892 days ago

  • NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads

    NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file containing both the corrected contigs and the correct, u...

    Tags: NxRepair, error, correction, denovo, assembly, Nextera, Mate, Pair, Reads

    1890 days ago

  • Genome assembly forensics: finding the elusive mis-assembly

    We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pi...

    Tags: Genome, assembly, forensics, elusive, mis-assembly

    1888 days ago

  • Evaluation of genome assembly software based on long reads

    TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence diversity. They have also been applied to resequencing...

    Tags: Evaluation, genome, assembly, software, long, reads

    1882 days ago