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Benchmarking short sequence mapping tools
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scholarly article
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
title
Benchmarking short sequence mapping tools
(English)
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
author
Amanda Ewart Toland
object named as
Amanda E Toland
series ordinal
3
0 references
Umit Catalyurek
object named as
Ümit V Çatalyürek
series ordinal
4
0 references
author name string
Ayat Hatem
series ordinal
1
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
Doruk Bozdağ
series ordinal
2
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
publication date
7 June 2013
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
published in
BMC Bioinformatics
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
volume
14
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
page(s)
184
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
exact match
https://scigraph.springernature.com/pub.10.1186/1471-2105-14-184
0 references
cites work
Tools for mapping high-throughput sequencing data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
RazerS 3: faster, fully sensitive read mapping
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Fast gapped-read alignment with Bowtie 2
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
GemSIM: general, error-model based simulator of next-generation sequencing data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
SOAP3: ultra-fast GPU-based parallel alignment tool for short reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
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7 July 2018
ART: a next-generation sequencing read simulator.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Comparative analysis of algorithms for next-generation sequencing read alignment
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
A novel and well-defined benchmarking method for second generation read mapping
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
mrsFAST: a cache-oblivious algorithm for short-read mapping.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
A survey of sequence alignment algorithms for next-generation sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
A human gut microbial gene catalogue established by metagenomic sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
High quality SNP calling using Illumina data at shallow coverage.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Fast and SNP-tolerant detection of complex variants and splicing in short reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
BFAST: an alignment tool for large scale genome resequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Sense from sequence reads: methods for alignment and assembly
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Personalized copy number and segmental duplication maps using next-generation sequencing.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
RazerS--fast read mapping with sensitivity control
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
SHREC: a short-read error correction method
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
SOAP2: an improved ultrafast tool for short read alignment
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
SHRiMP: accurate mapping of short color-space reads
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Fast and accurate short read alignment with Burrows-Wheeler transform
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
SNP detection for massively parallel whole-genome resequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Mapping short DNA sequencing reads and calling variants using mapping quality scores
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
ZOOM! Zillions of oligos mapped
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Using quality scores and longer reads improves accuracy of Solexa read mapping
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
SNPdetector: a software tool for sensitive and accurate SNP detection
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Intron-exon structures of eukaryotic model organisms
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Base-calling of automated sequencer traces using phred. II. Error probabilities
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Base-calling of automated sequencer traces using phred. I. Accuracy assessment
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
7 July 2018
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
26 October 2018
PASS: a program to align short sequences.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
26 October 2018
Slider--maximum use of probability information for alignment of short sequence reads and SNP detection
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694458
retrieved
26 October 2018
Identifiers
DOI
10.1186/1471-2105-14-184
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
DBLP publication ID
journals/bmcbi/HatemBTC13
1 reference
stated in
DBLP Dataset 2021-01-02
retrieved
28 January 2021
Dimensions Publication ID
1018663507
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release_cyuf6xympvatnmyto2mhamkhdi
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Fatcat
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https://api.fatcat.wiki/v0/release/cyuf6xympvatnmyto2mhamkhdi
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24 November 2022
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PMCID
3694458
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Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
PubMed ID
23758764
1 reference
stated in
Europe PubMed Central
PubMed ID
23758764
retrieved
4 August 2017
ResearchGate publication ID
237839657
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