This repository intends to be a collective effort towards the construction of a useful catalog of tools appropriate to use on long-read sequencing data.

• Filtlong - quality filtering tool for long reads
• chopper - intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file

• minimap 2 - A fast sequence mapping and alignment program

Comparison available here.

• Unicycler - hybrid assembly pipeline for bacterial genomes (miniasm and spades with racon and pilon for polishing)
• miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)
• canu - A single molecule sequence assembler for genomes large and small
• Flye - Fast and accurate de novo assembler for single molecule sequencing reads

• Racon - Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.

• Sniffles - structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)

Comparison available here

• Badread - a long read simulator that can imitate many types of read problems
• LongISLND - Long In silico Sequencing of Lengthy and Noisy Datatypes
• SiLiCO - a simulator of long read sequencing in pacbio and oxford nanopore

• MetaMaps - simultaenously carries out read assignment and sample composition estimation
• krocus - MLST from long reads
• ngmlr - long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
• MEGAN-LR - long-read and contig binning algorithm
• MAIRA - real-time taxonomic and functional analysis of long reads on a laptop

• NanoPlot - Plots and Statistics for quality evaluation
• NanoQC - Quality control tools for long read sequencing data aiming to replicate some of the plots made by fastQC
• NanoStat - Simple statistic summary
• Porechop - adapter trimmer and demultiplexer for Oxford Nanopore reads (abandonware since Oct 2018)
• poretools - a toolkit for working with Oxford nanopore data
• MinIONQC - fast and simple quality control for MinION sequencing data
• nanofilt - Filtering and trimming of long read sequencing data

Comparison available here.

• Albacore - Oxford Nanopore's official command-line basecaller (requires account)
• Guppy - GPU basecaller (in development)
• Scrappie - research basecaller
• DeepNano - developed by Vladimír Boža and colleagues at Comenius University
• Chiron - third-party basecaller developed by Haotian Teng and others in Lachlan Coin's group at the University of Queensland

• Deepbinner - a signal-level demultiplexer for Oxford Nanopore reads
• Porechop - adapter trimmer and demultiplexer for Oxford Nanopore reads (abandonware since Oct 2018)
• Albacore - Oxford Nanopore's official command-line basecaller (requires account)
• qcat - Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files

• nanopolish - Software package for signal-level analysis of Oxford Nanopore sequencing data.
• npScarf - scaffolds and completes draft genomes assemblies (spades) in real-time with Oxford Nanopore sequencing.

• nanoSV - SV caller for long-read (only tested in nanopore)

• NanoSim - Nanopore sequence read simulator

• nanocomp - Comparison of multiple long read datasets

• proovread - PacBio hybrid error correction through iterative short read consensus

• lima - Lima, the PacBio barcode demultiplexer, is the standard tool to identify barcode sequences in PacBio single-molecule sequencing data.

• blasr - The PacBio® long read aligner

• PBSIM - This is an updated mirror of the original PacBio Read Simulator

• pb-jelly - highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles.