- Home
- Publications
- Publication Search
- Publication Details
Title
PACVr: plastome assembly coverage visualization in R
Authors
Keywords
-
Journal
BMC BIOINFORMATICS
Volume 21, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2020-05-24
DOI
10.1186/s12859-020-3475-0
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes
- (2019) Stephan Greiner et al. NUCLEIC ACIDS RESEARCH
- An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity
- (2019) Badr Benjelloun et al. Molecular Ecology Resources
- Long-reads reveal that the chloroplast genome exists in two distinct versions in most plants
- (2019) Weiwen Wang et al. Genome Biology and Evolution
- Plastid phylogenomic analysis of green plants: A billion years of evolutionary history
- (2018) Matthew A. Gitzendanner et al. AMERICAN JOURNAL OF BOTANY
- Interactive and coordinated visualization approaches for biological data analysis
- (2018) António Cruz et al. BRIEFINGS IN BIOINFORMATICS
- The State of Software for Evolutionary Biology
- (2018) Diego Darriba et al. MOLECULAR BIOLOGY AND EVOLUTION
- The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae
- (2018) Ali Amiryousefi et al. PLoS One
- Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca
- (2018) Shigekatsu Suzuki et al. Scientific Reports
- Practical considerations for plant phylogenomics
- (2018) Michael R. McKain et al. Applications in Plant Sciences
- A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions
- (2018) Jeffery M. Saarela et al. PeerJ
- Organellar genome assembly methods and comparative analysis of horticultural plants
- (2018) Xuelin Wang et al. Horticulture Research
- Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping
- (2017) Joshua A. Udall et al. PLANT CELL
- What can we do with 1000 plastid genomes?
- (2017) Julian Tonti-Filippini et al. PLANT JOURNAL
- Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships
- (2017) Michael Gruenstaeudl et al. PLANT SYSTEMATICS AND EVOLUTION
- Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae
- (2017) Monique Turmel et al. Scientific Reports
- De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences
- (2017) Shairul Izan et al. Frontiers in Plant Science
- Indexcov: fast coverage quality control for whole-genome sequencing
- (2017) Brent S Pedersen et al. GigaScience
- Variable presence of the inverted repeat and plastome stability inErodium
- (2016) John C. Blazier et al. ANNALS OF BOTANY
- Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes
- (2016) Michael R. McKain et al. BIOINFORMATICS
- Strategies for complete plastid genome sequencing
- (2016) Alex D. Twyford et al. Molecular Ecology Resources
- NOVOPlasty:de novoassembly of organelle genomes from whole genome data
- (2016) Nicolas Dierckxsens et al. NUCLEIC ACIDS RESEARCH
- Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes
- (2015) Joseph F. Walker et al. AMERICAN JOURNAL OF BOTANY
- Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline
- (2015) Freek T. Bakker et al. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
- misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
- (2015) Xiao Zhu et al. BMC BIOINFORMATICS
- Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats
- (2015) Shiliang Hu et al. BMC GENOMICS
- Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae
- (2015) Monique Turmel et al. Genome Biology and Evolution
- Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?
- (2015) N. Scarcelli et al. Molecular Ecology Resources
- Orchestrating high-throughput genomic analysis with Bioconductor
- (2015) Wolfgang Huber et al. NATURE METHODS
- Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates
- (2015) Andan Zhu et al. NEW PHYTOLOGIST
- Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species
- (2015) Kyunghee Kim et al. Scientific Reports
- Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP
- (2015) Diana V. Dugas et al. Scientific Reports
- Software in the scientific literature: Problems with seeing, finding, and using software mentioned in the biology literature
- (2015) James Howison et al. Journal of the Association for Information Science and Technology
- Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
- (2015) Ruibang Luo et al. GigaScience
- Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes
- (2015) Zhiqiang Wu et al. PLoS One
- Correction: The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene
- (2015) Anna V. Williams et al. PLoS One
- Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
- (2014) D. H. Phanstiel et al. BIOINFORMATICS
- Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG
- (2014) Jonathan Crabtree et al. BIOINFORMATICS
- Toward better understanding of artifacts in variant calling from high-coverage samples
- (2014) Heng Li BIOINFORMATICS
- A field guide to whole-genome sequencing, assembly and annotation
- (2014) Robert Ekblom et al. Evolutionary Applications
- Sequencing depth and coverage: key considerations in genomic analyses
- (2014) David Sims et al. NATURE REVIEWS GENETICS
- Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs
- (2014) Dapeng Wang et al. NUCLEIC ACIDS RESEARCH
- Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice
- (2014) Nadja Korotkova et al. PLoS One
- QUAST: quality assessment tool for genome assemblies
- (2013) Alexey Gurevich et al. BIOINFORMATICS
- CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes
- (2013) Jinkui Cheng et al. BMC BIOINFORMATICS
- RCircos: an R package for Circos 2D track plots
- (2013) Hongen Zhang et al. BMC BIOINFORMATICS
- Sequence assembly demystified
- (2013) Niranjan Nagarajan et al. NATURE REVIEWS GENETICS
- OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets
- (2013) Marc Lohse et al. NUCLEIC ACIDS RESEARCH
- Contradiction between Plastid Gene Transcription and Function Due to Complex Posttranscriptional Splicing: An Exemplary Study of ycf15 Function and Evolution in Angiosperms
- (2013) Chao Shi et al. PLoS One
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
- (2012) M. Kearse et al. BIOINFORMATICS
- Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis
- (2012) Sophie Schbath et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- The case for open computer programs
- (2012) Darrel C. Ince et al. NATURE
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
- (2011) Guillaume Marçais et al. BIOINFORMATICS
- The evolution of the plastid chromosome in land plants: gene content, gene order, gene function
- (2011) Susann Wicke et al. PLANT MOLECULAR BIOLOGY
- Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects
- (2010) Lei GAO et al. Journal of Systematics and Evolution
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
- (2009) Ken Chen et al. NATURE METHODS
- GenomeVx: simple web-based creation of editable circular chromosome maps
- (2008) G. C. Conant et al. BIOINFORMATICS
- GBParsy: A GenBank flatfile parser library with high speed
- (2008) Tae-Ho Lee et al. BMC BIOINFORMATICS
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now