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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
poRe [37] Sequence extraction and basic statistics
BWA MEM [49] Sequence alignment
LAST [48] Sequence alignment
NanoOK [20] Sequence alignment, statistics, and visualization
marginAlign [9] Sequence alignment, SNV calling, and statistics
Nanopolish [50] Signal alignment and SNV calling
GraphMap [12] Sequence alignment and SNV calling
minimap Fast approximate mapping
miniasm De novo assembly
CANU [70] De novo assembly
Nanocorrect [48] De novo assembly
PoreSeq [53] De novo assembly and SNV calling
NaS [23] De novo assembly
Nanocorr [13] De novo assembly
Mash [71] Species identification and fast approximate alignments
minoTour [72] Real-time data analysis
Read Until [43] Selective sequencing
Nanocall [46] Local base-calling
DeepNano [47] Recurrent neural network (RNN)-based base-calling
  1. SNV single nucleotide variant