PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples (Q34182467)

31 July 2017

title

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples (English)

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31 July 2017

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Eduardo Castro-Nallar

object named as

Eduardo Castro-Nallar

6

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Keith A. Crandall

object named as

Keith A Crandall

7

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author name string

Changjin Hong

1

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31 July 2017

Solaiappan Manimaran

2

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31 July 2017

Ying Shen

3

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31 July 2017

Joseph F Perez-Rogers

4

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31 July 2017

Allyson L Byrd

5

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31 July 2017

William Evan Johnson

8

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31 July 2017

publication date

5 September 2014

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31 July 2017

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31 July 2017

volume

2

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31 July 2017

page(s)

33

1 reference

https://scigraph.springernature.com/pub.10.1186/2049-2618-2-33

31 July 2017

exact match

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cites work

Pathoscope: species identification and strain attribution with unassembled sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Scalable metagenomic taxonomy classification using a reference genome database

28 July 2018

1 reference

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A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Fast gapped-read alignment with Bowtie 2

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

The NIH Human Microbiome Project

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

The Sequence Alignment/Map format and SAMtools

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Phylogenetic classification of short environmental DNA fragments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Accurate phylogenetic classification of variable-length DNA fragments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Metagenomic microbial community profiling using unique clade-specific marker genes

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Rapid identification of non-human sequences in high-throughput sequencing datasets.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Pathogen detection using short-RNA deep sequencing subtraction and assembly

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

MEGAN analysis of metagenomic data

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4164323

High-speed microbial community profiling

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25225611

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/2049-2618-2-33

1 reference

Dimensions Publication ID

31 July 2017

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31 July 2017

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