Table of contents

• Installation
  • Quickstart
  • Conda
  • Docker
  • Manual installation
• User guide
  • Basic usage
  • Read processing
  • Removing adapters
  • Modifying reads
  • Filtering reads
  • Trimming paired-end reads
  • Multiple adapters
  • Illumina TruSeq
  • Dealing with N bases
  • Read merging and overwriting
  • Order of modifications
  • Bisulfite sequencing
  • Micro-RNA sequencing
  • Multi-threading
  • Atropos’s output
  • Quality control statistics
  • Adapter detection
  • Error rate estimation
• Colorspace reads
  • Ambiguity in colorspace
  • Double-encoding, BWA and MAQ
  • Colorspace examples
  • Bowtie
  • Sequence Read Archive
• Recipes
  • Forcing matches to be at the end of the read
  • Removing more than one adapter
  • Trimming poly-A tails
  • Other things (unfinished)