LOCAS specifications

Information


Unique identifier OMICS_00019
Name LOCAS
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 Juliane Klein

Publication for LOCAS

LOCAS citations

 (2)
library_books

An optimized approach for local de novo assembly of overlapping paired end RAD reads from multiple individuals

2018
R Soc Open Sci
PMCID: 5830760
PMID: 29515871
DOI: 10.1098/rsos.171589

[…] have assembled RPE reads into contigs using different assembly tools [,,], such as the de Bruijn Graph (DBG) based software Velvet [] and the Overlap-Layout-Consensus (OLC) based software CAP3 [] and LOCAS []. Davey et al. [] demonstrated that VelvetOptimiser was the best assembly tool for RAD data by comparing nine assembly tools. However, Hohenlohe et al. [] found CAP3 performed much better than […]

library_books

Special features of RAD Sequencing data: implications for genotyping

2012
Mol Ecol
PMCID: 3712469
PMID: 23110438
DOI: 10.1111/mec.12084

[…] 2 sequences by locus or by allele and test assembly accordingly. As expected based on previous reports (Baxter et al. ; Willing et al. ), unoptimizing assemblers such as Velvet (Zerbino & Birney, ), LOCAS (Klein et al. ) and SOAPdenovo (Li et al. ) produce poor assemblies, because of considerable variation in coverage and heterozygosity across RAD loci. VelvetOptimiser produces the best assemblie […]

LOCAS institution(s)
Chair of Algorithms in Bioinformatics, University of Tübingen, Tübingen, Germany; Genes and Disease Program, Center for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Spain; Department of Plant Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Köln, Germany; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany

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