OSLay protocols

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OSLay specifications

Information


Unique identifier OMICS_06932
Name OSLay
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for OSLay

OSLay in pipelines

 (5)
2014
PMCID: 3886955
PMID: 24407642
DOI: 10.1128/genomeA.01134-13

[…] resulted in 61,462,320 reads of 6,207,694,320 bases., the genome was assembled, de novo, by use of soapdenovo assembler v 1.05 (). the long assembly and the order of the contigs were generated by oslay (), with genome coverage of about 1,200×. the draft assembly of msp20.1 (g+c content of 36.47%) resulted in an approximate genome size of 4,363,086 bases. the draft genome consists of 78 […]

2013
PMCID: 3668006
PMID: 23723398
DOI: 10.1128/genomeA.00296-13

[…] 23-fold genome coverage for both strains. de novo genome assembly was performed using the newbler assembler 2.7 (roche diagnostics). the contigs were then oriented and ordered into scaffolds using oslay (). gene identification and automatic functional annotation were performed using the rast (rapid annotations using subsystem technology) server and blast2go (, ). the antibiotic resistomes […]

2013
PMCID: 3675517
PMID: 23792750
DOI: 10.1128/genomeA.00327-13

[…] produced, with a deep coverage of 605-fold. the short-read quality was determined using fastqc and clcbio workbench version 6.0. a total of 73 contigs were produced using clcbio de novo assembly. oslay software () was used to assemble the contigs into 4 scaffolds for the draft genome of this p. mirabilis strain pr03. the draft genome was viewed using artemis software (). the genome […]

2013
PMCID: 3744669
PMID: 23950113
DOI: 10.1128/genomeA.00418-13

[…] the sequences of k. pneumoniae ntuh-k2044, and 84.7% of reads matched the sequences of k. pneumoniae mgh 78578., scaffolds were generated using optimal synteny layout of unfinished assemblies (oslay) () and were remapped against the raw sequence (101 bp) to validate the assembly result. oslay showed that 41 out of 300 contigs were not part of the scaffolds. the total number of gaps was 85. […]

2010
PMCID: 3091624
PMID: 20507619
DOI: 10.1186/1471-2164-11-335

[…] of strain b8 using the nucmer program from the mummer software suite []. more precisely, nucmer computed maximal matches of minimum length 18. the resulting .coords-file was read by the program oslay []. this delivered an optimal syntenic layout of 71 b128-supercontigs relative to the genome sequence of strain b8. the remaining two supercontigs (supercontig 146 and supercontig 161) […]


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OSLay in publications

 (20)
PMCID: 5571417
PMID: 28839031
DOI: 10.1128/genomeA.00853-17

[…] (genbank accession no. ba000033) () by clc genomics workbench (clc bio, arthus, denmark), with an average 78-read mapping coverage. after the reads were assembled, contigs were aligned to mw2 with oslay (). gap closing was performed by sanger sequencing. only the gap within a cell wall protein corresponding to mw2416 remained, because this gene had a long g5-e repeat (), but we confirmed […]

PMCID: 4932478
PMID: 27110816
DOI: 10.3390/pharmaceutics8020015

[…] at base level, a post-assembly approach is designed to improve the quality through the following major functions: (1)contigs orientation and visualization. tools such as contiguator, projector2, oslay, and r2cat could are to visualize and arrange contigs and estimate gaps compared with a reference genome [,,,].(2)extending contigs and filling gaps. tools such as gaa program […]

PMCID: 4664717
PMID: 26697353
DOI: 10.1016/j.gdata.2015.08.028

[…] fastqc. de novo assembly was performed using soapdenovo v1.05, producing a total of 1486 contigs, which was used to construct 679 scaffolds. ordering and orienting of the scaffolds were done using oslay against four reference strains: acicu, aye, sdf, and atcc 17978. the optimal synteny was obtained when aligned against strain aye, and the subsequent analyses were done using that output. […]

PMCID: 4263841
PMID: 25502679
DOI: 10.1128/genomeA.01296-14

[…] workbench version 7.0.4. the total read length was 312,737,826 nt with an average coverage of 164.03×, and the consensus length was 1,756,717 nt. optimal syntenic layout of unfinished assemblies (oslay) was used to validate the assembly results with the reference genomes, and the total number of gaps was 55., the total sequences (cdss) were predicted by genemarks (), and trnas and rrnas […]

PMCID: 4148954
PMID: 25197474
DOI: 10.4056/sigs.3887716

[…] assembled using clcbio genomics workbench (clc bio, aarhus, denmark). one hundred and ninety-five contigs (n50: 13,272 bp) were generated, and were overlaid with the reference sequence mu50 using oslay. fourteen supercontigs were generated as a result. gaps were closed using sanger sequencing., the genome was annotated using basys [] and rast []., the mrsa pr01 genome consists […]


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OSLay institution(s)
Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, Tübingen, Germany

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