Xander: employing a novel method for efficient gene-targeted metagenomic assembly (Q35920493)

11 August 2017

Xander: employing a novel method for efficient gene-targeted metagenomic assembly (English)

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11 August 2017

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C Titus Brown

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James M Tiedje

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11 August 2017

Qiong Wang

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11 August 2017

Jordan A Fish

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11 August 2017

Mariah Gilman

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11 August 2017

Yanni Sun

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11 August 2017

James R Cole

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5 August 2015

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describes a project that uses

11 August 2017

MIRA

object named as

Mira

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Tackling soil diversity with the assembly of large, complex metagenomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

FunGene: the functional gene pipeline and repository

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

The future is now: single-cell genomics of bacteria and archaea

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Impact of different bioenergy crops on N-cycling bacterial and archaeal communities in soil

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

How to apply de Bruijn graphs to genome assembly

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

FLASH: fast length adjustment of short reads to improve genome assemblies

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

UCHIME improves sensitivity and speed of chimera detection

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

FragGeneScan: predicting genes in short and error-prone reads

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

A human gut microbial gene catalogue established by metagenomic sequencing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

A new generation of homology search tools based on probabilistic inference

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Fast and accurate short read alignment with Burrows-Wheeler transform

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

A bioinformatician's guide to metagenomics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

What is a hidden Markov model?

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Environmental genome shotgun sequencing of the Sargasso Sea

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Comparative genome assembly.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4526283

Space/time trade-offs in hash coding with allowable errors

24 September 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40168-015-0093-6

A Formal Basis for the Heuristic Determination of Minimum Cost Paths

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40168-015-0093-6

Finding theKShortest Loopless Paths in a Network

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40168-015-0093-6

A Procedure for Computing theKBest Solutions to Discrete Optimization Problems and Its Application to the Shortest Path Problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40168-015-0093-6

10.1186/S40168-015-0093-6

21 January 2018

Identifiers

DOI

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Dimensions Publication ID

11 August 2017

0 references

1 reference

11 August 2017

PubMed publication ID

26246894

1 reference