Tools

Nanopype integrates a growing number of different tools merged into processing workflows for common use cases.

Processing

Basecalling

• Albacore (access restricted to ONT community, manual install required)
• Guppy
• Flappie https://github.com/nanoporetech/flappie

Alignment

• Minimap2 https://github.com/lh3/minimap2
• Graphmap2 https://github.com/lbcb-sci/graphmap2
• Ngmlr https://github.com/philres/ngmlr

Analysis

Assembly

• Flye https://github.com/fenderglass/Flye
• Wtdbg2 https://github.com/ruanjue/wtdbg2

Methylation detection

• Nanopolish https://github.com/jts/nanopolish
• Flappie https://github.com/nanoporetech/flappie

Transcriptome

• Pinfish https://github.com/nanoporetech/pinfish

Structural variation

• Sniffles https://github.com/fritzsedlazeck/Sniffles
• SVIM https://github.com/eldariont/svim

Demultiplexing

• Deepbinner https://github.com/rrwick/Deepbinner

Miscellaneous

• Samtools https://github.com/samtools/samtools
• Bedtools https://github.com/arq5x/bedtools2
• UCSCTools http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
  • bedGraphToBigWig

Plugins:

* Winnowmap: *https://github.com/marbl/Winnowmap*