atropos
1.1
  • Installation
  • User guide
  • Colorspace reads
  • Recipes
atropos
  • Docs »
  • Table of contents
  • Edit on GitHub

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)
Next

© Copyright Original Cutadapt code: 2010-2014, Marcel Martin; Atropos modifications and improvements: 2015-2018, John P Didion Revision c4affb0d.

Built with Sphinx using a theme provided by Read the Docs.
Read the Docs v: 1.1
Versions
1.1
Downloads
On Read the Docs
Project Home
Builds

Free document hosting provided by Read the Docs.