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Trimmomatic: a flexible trimmer for Illumina sequence data
Oxford University Press | 2014|Publisher: Oxford University Press -
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Oxford University Press | 2015|Publisher: Oxford University Press -
Prokka: rapid prokaryotic genome annotation
Oxford University Press | 2014|Publisher: Oxford University Press -
Roary: rapid large-scale prokaryote pan genome analysis
Oxford University Press | 2015|Publisher: Oxford University Press -
The Sequence Alignment/Map format and SAMtools
Oxford University Press | 2009|Publisher: Oxford University Press -
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Oxford University Press | 2015|Publisher: Oxford University Press -
STAMP: statistical analysis of taxonomic and functional profiles
Oxford University Press | 2014|Publisher: Oxford University Press -
UCHIME improves sensitivity and speed of chimera detection
Oxford University Press | 2011|Publisher: Oxford University Press -
Fast and accurate short read alignment with Burrows-Wheeler transform
Oxford University Press | 2009|Publisher: Oxford University Press -
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels
Oxford University Press | 2015|Publisher: Oxford University Press -
circlize implements and enhances circular visualization in R
Oxford University Press | 2014|Publisher: Oxford University Press -
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
Oxford University Press | 2015|Publisher: Oxford University Press -
The variant call format and VCFtools
Oxford University Press | 2011|Publisher: Oxford University Press -
LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants
Oxford University Press | 2015|Publisher: Oxford University Press -
FLASH: fast length adjustment of short reads to improve genome assemblies
Oxford University Press | 2011|Publisher: Oxford University Press -
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
Oxford University Press | 2014|Publisher: Oxford University Press -
AliView: a fast and lightweight alignment viewer and editor for large datasets
Oxford University Press | 2014|Publisher: Oxford University Press -
Bandage: interactive visualization of de novo genome assemblies
Oxford University Press | 2015|Publisher: Oxford University Press -
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
Oxford University Press | 2015|Publisher: Oxford University Press -
Sambamba: fast processing of NGS alignment formats
Oxford University Press | 2015|Publisher: Oxford University Press