Orione

• Common Tools
  • Get data
  • NGS: quality control
  • NGS: manipulation
  • NGS: mapping
    • BLAT
  • NCBI BLAST+
• Microbiology
  • Get microbial data
  • NGS: RNA-seq for bacteria
    • EDGE-pro
  • NGS: de novo assembly
    • Velvet
    • ABySS
    • Edena
  • NGS: post assembly
    • Tools
    • SSPACE
    • SSAKE
    • SOPRA
    • SEQuel
    • MuMMer
    • Mugsy
  • Gene annotation
    • Glimmer
    • Prokka
    • tRNAscan
• Variant Calling
  • NGS: SNP effects
  • NGS: indel analysis
    • Filter Indels from SAM
    • Extract Indels from SAM
    • Indel Analysis Table
    • Indel Analysis
  • NGS: SAM tools
  • NGS: GATK tools
  • VCF tools
• Metagenomics
  • Metaphlan
  • Other tools
• NGS: RNA Analysis
  • RNA-seq
    • TopHat for Illumina
    • TopHat2
    • Cufflinks
    • Cuffcompare
    • Cuffmerge
    • Cuffdiff
  • Filter combined transcripts
  • miRNA prediction
• Chip-Seq
  • NGS: peak calling
    • MACS
    • MACS14
    • SICER
    • CCAT
    • GeneTrack indexer
    • Peak predictor
  • Motif tools
    • MEME
    • FIMO
    • Sequence logo
• Other tools
  • Text manipulation
  • FASTQ manipulation
  • FASTA manipulation
  • NGS: Picard (beta)
  • Filter and Sort
  • Join, Subtract and Group
  • Convert Formats
  • Operate on Genomic Intervals
  • NGS: Simulation
  • Evolution