Oxford Nanopore tools
List of long-read software long-read-tools.org
QC
Porechop
GCATemplates available: no
Porechop homepage
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.
Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.
module spider Porechop
Genome assembly
Unicycler
GCATemplates available: no
Unicycler is an assembly pipeline for bacterial genomes.
It circularises replicons without the need for a separate tool like Circlator.
It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
module spider Unicycler
wtdbg2
wtdbg2 homepage
WTDBG: De novo assembler for long noisy sequences
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.
module spider wtdbg2
Assembly polishing
Redundans
Redundans homepage
Redundans pipeline assists an assembly of heterozygous genomes. Program takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly. Final assembly should be less fragmented and with total size smaller than the input contigs. In addition, Redundans will automatically close the gaps resulting from genome assembly or scaffolding.
module spider Redundans
Racon
GCATemplates available: no
Consensus module for raw de novo DNA assembly of long uncorrected reads.
Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step.
module spider Racon
Nanopolish
GCATemplates available: no
Nanopolish homepage
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more.
module spider nanopolish
Sequence alignments
Minimap2
Minimap2 homepage
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
module spider minimap2
LAST
GCATemplates available: no
LAST homepage
module spider LAST
LAST finds similar regions between sequences. LAST copes more efficiently with repeat-rich sequences (e.g. genomes).
For example: it can align reads to genomes without repeat-masking, without becoming overwhelmed by repetitive hits.
Nanopolish
GCATemplates available: no
Nanopolish homepage
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more.
module spider nanopolish
Simulate Reads
NanoSim
NanoSim homepage
NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology.
module spider NanoSim