Nanopore software
Assembly
flye (recommended)
quick start: flye --nano-raw myreads.fasta --out-dir myassembly_nano --genome-size 5m --threads 4
Unicycler (Long-read only or hybrid)
SPAdes (hybrid)
MaSuRCA (hybrid)
Trycycler (consensus assembly)
Benchmark studies
Benchmarking of long-read assemblers for prokaryote whole genome sequencing
Metagenome assembly
Metagenome classification
DNA / RNA methylation / modification
Tombo (recommended; also visualises raw signal)
quick start
tombo resquiggle fast5/ genome.fasta --processes 4 --num-most-common-errors 5
tombo detect_modifications de_novo --fast5-basedirs fast5/ --stat-file-name sample.de_novo_detect --processes 4
Correction
Nanopolish (works on raw signal, can also detect base mods)
Medaka (neural networks, "50X faster than Nanopolish", works on .fastq)
Racon ("ultrafast consensus" with Illumina or ONT)
Pilon (Illumina)
NextPolish (Illumina)
MarginPolish (graph-based assembly polisher)
HELEN (Homopolymer Encoded Long-read Error-corrector for Nanopore, operates on pileup from Margin Polish)
Metabarcode / 16S / 18S / ITS
Epi2Me
pipeline by Anna Cusco from the paper on Microbiota profiling...
Variant calling
Nanopolish (works on raw signal, can also detect base mods)
Pipelines
reticulatus (assembly and polishing)
katuali (assembly and polishing)