Newmap documentation

Newmap is a set of tools for quantifying mappability for any sequence. Newmap records mers of length k if k is unique across the entire sequence. From these unique lengths, at given length k, Newmap can then output a single-read mappability Browser Extensible Data (BED) file and a multi-read mappability Wiggle file.

Contents

• Usage
• Installation
• Quickstart
  • Create an index for a reference sequence (genome.fa)
  • Find unique k-mer lengths for a chromosome (chr1.fna.gz)
  • Convert the minimum unique k-mer lengths to mappability output files
• Commands
  • index
    • Positional Arguments
    • Options
    • FM-index parameters
      • FM-index technical details
  • search
    • Positional Arguments
    • Output Options
    • Performance Options
      • K-mer search ranges
      • Ambiguous bases
      • Threading
  • track
    • Positional Arguments
    • Options
      • Mappability datasets
      • Single-read mappability
      • Multi-read mappability
• Unique File Format
  • Data types
  • Usage
• Umap
  • Umap dataset differences
    • unique.uint8
    • Mappability files
• Credits