Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. (Q52607244)

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scientific article published on 2 April 2018

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English	Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.	scientific article published on 2 April 2018

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scholarly article

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29617724 AND SRC:MED&resulttype=core&format=json

22 March 2020

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions (English)

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22 March 2020

4

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22 March 2020

5

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22 March 2020

author name string

Damla Senol Cali

1

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22 March 2020

Jeremie S Kim

2

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22 March 2020

Saugata Ghose

3

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22 March 2020

publication date

1 July 2019

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22 March 2020

Briefings in Bioinformatics

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22 March 2020

20

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22 March 2020

4

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Europe PubMed Central

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22 March 2020

1542-1559

1 reference

Europe PubMed Central

PMC publication ID

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22 March 2020

Improved tools for biological sequence comparison

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

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Hidden Markov models

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https://pubmed.ncbi.nlm.nih.gov/29617724

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Characterization of individual polynucleotide molecules using a membrane channel

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

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An Eulerian path approach to DNA fragment assembly

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Multiple sequence alignment using partial order graphs

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Mapping short DNA sequencing reads and calling variants using mapping quality scores

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

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The potential and challenges of nanopore sequencing

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https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Continuous base identification for single-molecule nanopore DNA sequencing

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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CloudBurst: highly sensitive read mapping with MapReduce

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Fast and accurate short read alignment with Burrows-Wheeler transform

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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SHRiMP: accurate mapping of short color-space reads

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Genome assembly reborn: recent computational challenges

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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The Sequence Alignment/Map format and SAMtools

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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RazerS--fast read mapping with sensitivity control

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Personalized copy number and segmental duplication maps using next-generation sequencing.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Fast and accurate long-read alignment with Burrows-Wheeler transform

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

mrsFAST: a cache-oblivious algorithm for short-read mapping.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Limitations of next-generation genome sequence assembly

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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SHRiMP2: Sensitive yet Practical Short Read Mapping

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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How to apply de Bruijn graphs to genome assembly

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Repetitive DNA and next-generation sequencing: computational challenges and solutions

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Tools for mapping high-throughput sequencing data

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Fast and accurate read mapping with approximate seeds and multiple backtracking

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Accelerating read mapping with FastHASH.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Benchmarking short sequence mapping tools

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Reducing assembly complexity of microbial genomes with single-molecule sequencing

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Ten years of next-generation sequencing technology

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Genome assembly using Nanopore-guided long and error-free DNA reads

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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A complete bacterial genome assembled de novo using only nanopore sequencing data

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

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Nanopores: a sequencer in your backpack

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Assessing the performance of the Oxford Nanopore Technologies MinION.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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MinION Analysis and Reference Consortium: Phase 1 data release and analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Real-time, portable genome sequencing for Ebola surveillance

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Fast and sensitive mapping of nanopore sequencing reads with GraphMap

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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On genomic repeats and reproducibility

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Nanocall: an open source basecaller for Oxford Nanopore sequencing data.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Oxford Nanopore MinION Sequencing and Genome Assembly

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Fast and accurate de novo genome assembly from long uncorrected reads.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Detecting DNA cytosine methylation using nanopore sequencing.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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DNA sequencing at 40: past, present and future

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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A sequencer coming of age: De novo genome assembly using MinION reads.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Nanopore sequencing and assembly of a human genome with ultra-long reads.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

1 reference

https://pubmed.ncbi.nlm.nih.gov/29617724

12 December 2020

based on heuristic

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Identifiers

10.1093/BIB/BBY017

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29617724 AND SRC:MED&resulttype=core&format=json

22 March 2020

0 references

DBLP publication ID

journals/bib/CaliKGAM19

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29617724 AND SRC:MED&resulttype=core&format=json

22 March 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29617724 AND SRC:MED&resulttype=core&format=json

22 March 2020

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