chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data

1 Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Germany 2 Center for Computational and Theoretical Biology, University of Würzburg 3 Department of Bioinformatics, University of Würzburg 4 Centre for Experimental Molecular Medicine, University Clinics Würzburg, Germany 5 Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany 6 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology 7 Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Applied Ecology and Bioresources, Gießen, Germany a These authors contributed equally to this work DOI: 10.21105/joss.00464

[1]  Alexander Richter,et al.  ChloroplastDB: the Chloroplast Genome Database , 2005, Nucleic Acids Res..

[2]  Aaron R. Quinlan,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[3]  Elizabeth A. Kellogg,et al.  Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes , 2016, Bioinform..

[4]  Xiaojuan Li,et al.  Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae) , 2016, Front. Plant Sci..

[5]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[6]  Xiaojun Guan,et al.  CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences , 2012, BMC Genomics.

[7]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[8]  Robert K. Jansen,et al.  Automatic annotation of organellar genomes with DOGMA , 2004, Bioinform..

[9]  Dmitry Antipov,et al.  plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data , 2016, bioRxiv.

[10]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[11]  Dmitry Antipov,et al.  Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads , 2013, RECOMB.

[12]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[13]  Pierre Taberlet,et al.  From barcodes to genomes: extending the concept of DNA barcoding , 2016, Molecular ecology.

[14]  Hideaki Sugawara,et al.  The Sequence Read Archive , 2010, Nucleic Acids Res..

[15]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..