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.