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PERGA specifications

Information


Unique identifier OMICS_10884
Name PERGA
Alternative name Paired-End Reads Guided Assembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Yadong Wang

Publication for Paired-End Reads Guided Assembler

PERGA citations

 (13)
library_books

A Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective

2018
Evol Bioinform Online
PMCID: 5826002
PMID: 29511353
DOI: 10.1177/1176934318758650

[…] e-end data sets. Ray showed second highest genome fraction with a mean of 58.8% followed by Velvet with third highest genome fraction with a mean of 57.1% on prokaryotic paired-end data sets, whereas Perga, Edena, and SGA showed average accuracy with a mean genome fraction of 51.9%, 51.4%, and 50.4% and SSAKE showed worst accuracy with mean genome fraction of 13.2%.On single-end prokaryotic data s […]

library_books

Genomic repeats, misassembly and reannotation: a case study with long read resequencing of Porphyromonas gingivalis reference strains

2018
BMC Genomics
PMCID: 5771137
PMID: 29338683
DOI: 10.1186/s12864-017-4429-4

[…] ces the longest contigs and the fewest per assembly. SPAdes and A5miseq are just behind, with very similar performances. The other assemblers generate more fragmented assemblies, and some (Velvet and PERGA) do not even seem suitable for this bacterial group (Fig. ). Closer examination of the results of the three assemblers producing the highest N50 (Fig. , upper panel) shows that the number of con […]

library_books

Vitamin D and Neurological Diseases: An Endocrine View

2017
Int J Mol Sci
PMCID: 5713448
PMID: 29160835
DOI: 10.3390/ijms18112482

[…] s [,], several studies have suggested a potential modulatory role for DBP in the development of MS [,,,,,], although DBP results in CSF or plasma have generated discrepant results [,,,,,,]. Recently, Perga et al. proposed a novel biomolecular tool consisting of two isoforms of DBP and ApoE in CSF, which may aid monitoring the progression of MS []. If validated in a larger population, this tool cou […]

library_books

Temperature controls organic carbon sequestration in a subarctic lake

2016
Sci Rep
PMCID: 5052527
PMID: 27708382
DOI: 10.1038/srep34780

[…] and N by 0.01‰. Determination of the stable isotopic composition of carbon and nitrogen in chitinous cladoceran (Chydoridae and Bosminidae) exoskeletons (δ13CChd/Bos, δ15NChd/Bos) was done following Perga. The sediments were heated with 10% potassium hydroxide (KOH) for 30 minutes to remove organic matter coating from the remains, followed by treatment with 1 M HCl to remove any carbonate coating […]

library_books

Molecular cloning, expression analysis and subcellular localization of four DELLA genes from hybrid poplar

2016
Springerplus
PMCID: 4951394
PMID: 27478746
DOI: 10.1186/s40064-016-2728-x

[…] AS family) of Arabidopsis, maize, rice and soybean were all intron- free (Xuan et al. ), but the homologous genes in Pinus contain introns (Laajanen et al. ).Multiple sequence alignments suggest that PeRGA1, PeRGA2, PeGAI1 and PeGAI2 all have DELLA motifs that contain the specific DELLA protein’s domain, and it is necessary for DELLA proteins to interact with GID1 (Sun et al. ). The phylogenetic a […]

library_books

Nitrogen fixation by cyanobacteria stimulates production in Baltic food webs

2015
PMCID: 4447702
PMID: 26022324
DOI: 10.1007/s13280-015-0660-x

[…] al. ; Lesutiene et al. ). In freshwater, application of FA markers has provided compelling evidence that toxic cyanobacterial blooms provide juvenile perch with components of high nutritional value (Perga et al. ). The authors concluded that the cyanobacterial bloom could be regarded as a significant dietary bonus for juvenile fish at a critical time of the year. Although the duration of this eff […]

Citations

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PERGA institution(s)
Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
PERGA funding source(s)
This work was partially supported by the National Nature Science Foundation of China (61173085, 61102149 and 11171086), the National High-Tech Research and Development Program (863) of China (2012AA020404, 2012AA02A602 and 2012AA02A604), the Hong Kong GRF (HKU 7111/12E, HKU 719709E and 719611E), the Shenzhen Basic Research Project (NO.JCYJ20120618143038947), and the Outstanding Researcher Award (102009124).

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