Nanopore software

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images from @iiSeymour and @samstudio8

Basecall

  • guppy (links to all ONT software, requires community login)

  • bonito (convolutional basecaller)

Demultiplex

Quality Control / visualisation

Filtering

Assembly

Benchmark studies

Benchmarking of long-read assemblers for prokaryote whole genome sequencing

Metagenome assembly

Metagenome classification

Mapping

  • minimap2 (recommended)

    • quick start: ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam

  • graphmap

    • quick start: graphmap align -r reference.fa -d reads.fasta -o output.sam

  • last (handles complex rearrangements and duplications in the reads)

  • bwa mem (now replaced by minimaps for ONT and PacBio)

RNA-seq

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

  • nanodisco

  • deepsignal

  • megalodon

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

Variant calling

Pipelines