11 Matching Annotations
  1. Jan 2023
  2. www.plasmidsaurus.com www.plasmidsaurus.com
    1. If the pipeline does not produce a consensus for your target, you can download the raw reads from your dashboard and bin them yourself, but please note that raw reads are much more noisy and error-prone (~98.3% accurate) than consensus reads.

      Look for binning tools - Example - LRBinner = reference free binning approach for nanopore. Ref : Wickramarachchi, Anuradha, and Yu Lin. "Binning long reads in metagenomics datasets using composition and coverage information." Algorithms for Molecular Biology 17.1 (2022): 1-15. bmc 202

  3. Oct 2022
    1. To perform bacterial genome assembly, we suggest using the third-party de novo assembly tool Flye3. This analysis package represents a complete pipeline, taking raw nanopore reads as input, and producing polished contigs as output. We also recommend one round of polishing with Medaka4. These tools can be found on GitHub
  4. Jun 2021
    1. As the speed of unperturbed electrophoretic polynucleotide passage precludes the resolution of individual nucleotides, a DNA- or RNA-binding motor enzyme is added to the system to gain a processive and slowed down passage (millisecond scale per nucleotide) of the polynucleotide through the nanopore
    2. single-stranded polynucleotide is electrophoretically threaded through a protein or solid-state nanopore.
    1. . For example, if a miscalling occurs at the end of a hairpin in a top strand read, the bottom strand read would correctly basecall this sequence before the hairpin is encountered

      strand bias example

    1. sequencing adapters, supplied in the kit, are ligated onto the prepared ends.

      What is the function of these adapters

  5. Mar 2021
    1. use of plasmid DNA enabled lower depth sequencing, and assemblies sufficient for full antimicrobial resistance gene annotation were obtained with as few as 2,000 to 5,000 reads, which could be acquired in 20 min of sequencing
  6. Apr 2020
    1. dA-tailing to add an “A” base to the 3′ end of the fragment
    2. Sequencing begins at the single-stranded 5′ end of the Y adapter, followed by the “template” strand
  7. Mar 2019
    1. Nanopore data and downstream anlysis

      In this post, only explain pass, fail and skip in nanopore sequencing.

  8. Nov 2018