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Table 1 Software tools developed specifically for MinION sequence data; there are existing tools that can also be made to work with nanopore data (not shown)

From: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

Name Applications Link
Poretools [22] Sequence data extraction and statistics https://github.com/arq5x/poretools
poRe [37] Sequence extraction and basic statistics https://sourceforge.net/projects/rpore/
BWA MEM [49] Sequence alignment https://github.com/lh3/bwa
LAST [48] Sequence alignment http://last.cbrc.jp/
NanoOK [20] Sequence alignment, statistics, and visualization https://documentation.tgac.ac.uk/display/NANOOK/
marginAlign [9] Sequence alignment, SNV calling, and statistics https://github.com/benedictpaten/marginAlign
Nanopolish [50] Signal alignment and SNV calling https://github.com/jts/nanopolish
GraphMap [12] Sequence alignment and SNV calling https://github.com/isovic/graphmap
minimap Fast approximate mapping https://github.com/lh3/minimap
miniasm De novo assembly https://github.com/lh3/miniasm
CANU [70] De novo assembly https://github.com/marbl/canu
Nanocorrect [48] De novo assembly https://github.com/jts/nanocorrect
PoreSeq [53] De novo assembly and SNV calling https://github.com/tszalay/poreseq
NaS [23] De novo assembly https://github.com/institut-de-genomique/NaS
Nanocorr [13] De novo assembly https://github.com/jgurtowski/nanocorr
Mash [71] Species identification and fast approximate alignments https://github.com/marbl/mash
minoTour [72] Real-time data analysis https://github.com/minoTour/minoTour
Read Until [43] Selective sequencing https://github.com/mattloose/RUscripts
Nanocall [46] Local base-calling https://github.com/mateidavid/nanocall
DeepNano [47] Recurrent neural network (RNN)-based base-calling https://bitbucket.org/vboza/deepnano
  1. SNV single nucleotide variant