Table 1.
List of analysis tools developed for Oxford Nanopore data
| Name | Applications | Link | Ref. |
|---|---|---|---|
| BWA | Fast nanopore data tuned alignment tool | https://github.com/lh3/bwa | [19] |
| GraphMap | Mapper for long and error-prone reads | https://github.com/isovic/graphmap | [25] |
| LAST | Nanopore tuned alignment tool | http://last.cbrc.jp/ | [20] |
| LINKS | Software tool for long read scaffolding | https://github.com/warrenlr/LINKS/ | [26] |
| marginAlign | Tools to align nanopore reads to a reference | https://github.com/benedictpaten/marginAlign | [27] |
| minoTour | Real time analysis tools | http://minotour.nottingham.ac.uk/ | [24] |
| nanoCORR | Error-correction tool for nanopore sequence data | https://github.com/jgurtowski/nanocorr | [28] |
| NanoOK | Software for nanopore data, quality and error profiles | https://documentation.tgac.ac.uk/display/NANOOK/NanoOK | [23] |
| Nanopolish | Nanopore analysis and genome assembly software | https://github.com/jts/nanopolish | [17] |
| nanopore | Variant-detection tool for nanopore sequence data | https://github.com/mitenjain/nanopore | [27] |
| Nanocorrect | Error-correction tool for nanopore sequence data | https://github.com/jts/nanocorrect/ | [29] |
| npReader | Real-time conversion and analysis of nanopore reads | https://github.com/mdcao/npReader | [30] |
| poRe | Tool for analyzing and visualizing nanopore data | https://sourceforge.net/p/rpore/wiki/Home/ | [22] |
| PoreSeq | Error-correction and variant-calling software | https://github.com/tszalay/poreseq | [31] |
| Poretools | Nanopore sequence analysis and visualization software | https://github.com/arq5x/poretools | [21] |
| SSPACE-LongRead | Genome scaffolding tool | http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread | [32] |
| SMIS | Genome scaffolding tool | https://sourceforge.net/projects/phusion2/files/smis/ | [33] |