(Q40548513)

21 September 2017

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs (English)

1 reference

21 September 2017

2

1 reference

21 September 2017

4

1 reference

21 September 2017

6

1 reference

21 September 2017

5

Matthew Berriman

1 reference

21 September 2017

Martin T Swain

1

1 reference

21 September 2017

Samual A Assefa

series ordinal

3

1 reference

21 September 2017

language of work or name

1 reference

7 June 2012

1 reference

21 September 2017

1 reference

21 September 2017

7

1 reference

21 September 2017

1260-1284

1 reference

21 September 2017

7

1 reference

https://scigraph.springernature.com/pub.10.1038/nprot.2012.068

21 September 2017

0 references

cites work

A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

GAGE: A critical evaluation of genome assemblies and assembly algorithms

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Graph accordance of next-generation sequence assemblies

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Cestode genomics - progress and prospects for advancing basic and applied aspects of flatworm biology

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Comparing de novo genome assembly: the long and short of it

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

The impact of next-generation sequencing on genomics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Next generation sequence assembly with AMOS.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Genotypic and phenotypic modifications of Neisseria meningitidis after an accidental human passage

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Rapid pneumococcal evolution in response to clinical interventions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Scaffolding pre-assembled contigs using SSPACE

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Limitations of next-generation genome sequence assembly

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Assembly algorithms for next-generation sequencing data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

The sequence and de novo assembly of the giant panda genome

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

The integrated microbial genomes system: an expanding comparative analysis resource

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Genomics. Genome project standards in a new era of sequencing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Next-generation DNA sequencing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Genome assembly forensics: finding the elusive mis-assembly

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Enhancements and modifications of primer design program Primer3.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Finishing the euchromatic sequence of the human genome

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Versatile and open software for comparing large genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Automated correction of genome sequence errors

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Hierarchical scaffolding with Bambus

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

SSAHA: a fast search method for large DNA databases

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Pyrosequencing sheds light on DNA sequencing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

RATT: Rapid Annotation Transfer Tool

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

r2cat: synteny plots and comparative assembly

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

ABACAS: algorithm-based automatic contiguation of assembled sequences

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

17 June 2018

Assembly reconciliation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

OSLay: optimal syntenic layout of unfinished assemblies.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

GARSA: genomic analysis resources for sequence annotation.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3648784

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

20 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2012.068

A System for Automated Bacterial (genome) Integrated Annotation--SABIA

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2012.068

Using the Velvet de novo assembler for short-read sequencing technologies

31 March 2020

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2012.068

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NPROT.2012.068

1 reference

Dimensions Publication ID

21 September 2017

0 references

1 reference

21 September 2017

1 reference