NanoPack: visualizing and processing long read sequencing data

Coster, Wouter De; D’Hert, Svenn; Schultz, Darrin T.; Cruts, Marc; Broeckhoven, Christine Van

doi:10.1101/237180

Cited by 33 publications

(32 citation statements)

References 16 publications

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“…Optionally, a reference gene annotation file (GFF) may be supplied to determine how many known genes could be retrieved from the assemblies. The quality of the read set is analyzed using Nanoplot [2] and aligned to the reference genome using Minimap2 (version 2.9-r720) [12]. The generated analysis reports are summarized by MultiQC [3] and can be shared on Github/Gitlab.…”

Section: Methodsunclassified

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poreTally: run and publish de novo Nanopore assembler benchmarks

Lannoy

Risse

Ridder

2018

Preprint

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Nanopore sequencing is a novel approach to nucleic acid analysis that generates long, error-prone reads. Since device components, base calling software and best practices for sample preparation are updated frequently and extensively, the nature of the produced data also changes frequently. As a result, peer-reviewed publications on de novo assembly pipeline benchmarking efforts are quickly rendered outdated by the next major improvement to the sequencing platforms. To provide the user community with a faster, more flexible alternative to peer-reviewed benchmark papers for de novo assembly tool performance we constructed poreTally, a comprehensive benchmarking tool. poreTally automatically assembles a given read set using several often-used assembly pipelines, analyzes the resulting assemblies for correctness and continuity, and finally generates a quality report. Results can immediately be shared with peers in a Github/Gitlab repository. Furthermore, we aim to give a more inclusive overview of assembly pipeline performance than any individual research group can, by offering users the possibility to submit their results to a collective benchmarking effort. poreTally is available on Github.

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Section: Methodsunclassified

“…Nanoplot [2] is used to assess raw read length and quality scores. Minimap2 [12] then maps the reads to the reference genome to estimate deletion, insertion and substitution error rates.…”

Section: Pipeline Performance Analysismentioning

confidence: 99%

poreTally: run and publish de novo Nanopore assembler benchmarks

Lannoy

Risse

Ridder

2018

Preprint

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“…After demultiplexing, 2.79 Gb of data were assigned to C. metapsilosis MSK414. Read quality was checked with NanoPlot version 1.23.1 (De Coster et al 2018). Potential contaminant reads (i.e.…”

Section: Dna Extraction and Illumina Sequencingmentioning

confidence: 99%

Identification of a novel Candida metapsilosis isolate suggests ongoing hybridization.

O’Brien

Zhai

Ola

et al. 2021

Preprint

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Candida metapsilosis is a member of the C. parapsilosis species complex, a group of opportunistic human pathogens. Of all the members of this complex, C. metapsilosis is the least virulent, and accounts for a small proportion of invasive Candida infections. Previous studies established that all C. metapsilosis isolates are hybrids, originating from a single hybridization event between two lineages, parent A and parent B. Here, we use MinION and Illumina sequencing to characterize a C. metapsilosis isolate that originated from a separate hybridization. One of the parents of the new isolate is very closely related to parent A. However, the other parent (parent C) is not the same as parent B. Unlike C. metapsilosis AB isolates, the C. metapsilosis AC isolate has not undergone introgression at the Mating Type-like Locus. In addition, the A and C haplotypes are not fully collinear. The C. metapsilosis AC isolate has undergone Loss of Heterozygosity (LOH) with a preference for haplotype A, indicating that this isolate is in the early stages of genome stabilization.

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“…After sequencing, we used Guppy (version 2.3.5) (ONT) with default settings to convert raw signal intensity data into base calls. We kept all nanopore reads with a length greater than 500 bp and trimmed them for adapter sequences with NanoPack (De Coster et al 2018). We used Canu (version 1.7) (Koren et al 2017) to correct base calls in the low quality of nanopore raw reads.…”

Section: Strain Information and Sequencingmentioning

confidence: 99%

Improved Reference Genome forCyclotella CrypticaCCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

Roberts

Downey

Ruck

et al. 2020

Preprint

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The diatom, Cyclotella cryptica, is a well-established experimental model for physiological studies and, more recently, biotechnology applications of diatoms. To further facilitate its use as a model diatom species, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long-and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms. 4

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NanoPack: visualizing and processing long read sequencing data

Cited by 33 publications

References 16 publications

poreTally: run and publish de novo Nanopore assembler benchmarks

poreTally: run and publish de novo Nanopore assembler benchmarks

Identification of a novel Candida metapsilosis isolate suggests ongoing hybridization.

Improved Reference Genome forCyclotella CrypticaCCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

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