Long-read sequencing Tools

The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.

Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads.

HELEN (Homopolymer Encoded Long-read Error-corrector for Nanopore) is a highly optimized genome polishing pipeline that uses deep learning to correct errors in Nanopore long-read assemblies, working in conjunction with MarginPolish and supporting GPU acceleration for scalability.

Homopolish is a method for the removal of systematic errors in nanopore sequencing by homologous polishing.

IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores.

IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique.

The Long Read Aligner for Sequences and Contigs. LRA, the long read aligner for sequences and assembly contigs LRA is a sequence alignment program that aligns long reads from single-molecule sequencing (SMS) instruments, or megabase-scale contigs from SMS assemblies. LRA implements seed chaining sparse dynamic programming with a convex gap function to read and assembly alignment, which is also extended to allow for inversion cases. Through the Truvari analysis of LRA, Minimap2 and NGM-LR alignments. LRA achieves higher f1 score over HG002 HiFi, CLR and ONT datasets. Home: https://github.com/ChaissonLab/LRA. Long read aligner for sequences and contigs.

LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. It can produce nearly chromosome-scale haplotype blocks by using Nanpore ultra-long reads without the need for additional trios, chromosome conformation, and strand-seq data. LongPhase can phase a 30x human genome in ~1 minute

LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc.

MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly.

Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.

Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

NanoFilt is a streaming filtering tool for Oxford Nanopore sequencing data in FASTQ format, enabling filtering based on minimum read quality, length, and GC content, as well as trimming of nucleotides from read ends.

NanoLyse is a streaming tool for removing contaminant DNA reads (such as lambda phage control DNA) from Oxford Nanopore FASTQ files using the Minimap2 aligner, with minimal memory footprint for integration into sequencing pipelines.

NanoPlot is a visualization tool for long-read sequencing data producing various plots including read length histograms, quality score distributions, and bivariate plots for Oxford Nanopore and PacBio data in FASTQ, BAM, or summary file formats.

Nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data, supporting genome assembly polishing, variant calling, methylation detection, and other analyses using raw electrical signal data from the sequencer.

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data. This results in greater yield of high-quality reads.

lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data. It powers the Demultiplex Barcodes GUI-based analysis applications.