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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.

PopIns2 is a tool for population-scale detection of non-reference sequence variants using colored de Bruijn Graphs.

Fast Hybrid Assembly of Long Reads. HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. HASLR is capable of assembling large genomes on a single computing node. Our experiments show that it can assemble a CHM1 human dataset in less than 10 hours using 64 CPU threads.

A probabilistic method for filling gaps in genome assemblies.

Fast and lightweight assembly-guided scaffolding using minimizer graphs. Scaffolding draft assemblies using reference assemblies and minimizer graphs. ntJoin takes a target assembly and one or more 'reference' assembly as input, and uses information from the reference(s) to scaffold the target assembly. The 'reference' assemblies can be true reference assembly builds, or a different draft genome assemblies.

Minimizer-based Sparse de Bruijn Graph Construction. Minimizer based sparse de Bruijn Graph constructor. Homopolymer compress input sequences, pick syncmers from hpc-compressed sequences, connect syncmers with an edge if they are adjacent in a read, unitigify. Suggested input is PacBio HiFi/CCS reads. May or may not work with Illumina reads. Algorithmic details: https://www.biorxiv.org/content/10.1101/2020.09.18.303156v1.

Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s). Cuttlefish is a tool for constructing the (colored) compacted de Bruijn graph from a collection of one or more genome references. Cuttlefish introduces a novel modeling scheme of the de Bruijn graph vertices as finite-state automata, and constrains the state-space for the automata to enable tracking of their transitioning states with very low memory usage. Cuttlefish is also fast and highly parallelizable. Experimental results demonstrate that the algorithm scales much better than existing approaches, especially as the number and scale of the input references grow.

a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme | A scaffold assemble pipeline for stLFR reads | This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds | git clone --recursive https://github.com/BGI-QingDao/SLR-superscaffolder.git YOUR-DOWNLOAD-DIR --depth 10 | Here is an illustration of this pipeline:

Assembling Centromeres with Long Error-Prone Reads | An algorithm for centromere assembly using long error-prone reads | Scripts for analyses and figures for centroFlye manuscript | centroFlye is an algorithm for centromere assembly using long error-prone reads. Currently it supports assembly of a human centromere X. Here we show how to apply it for the centromere X of the CHM13hTERT human cell line | Results_and_several_Appendices.ipynb replicates Results and Appendices: Analysis of centromeric reads that do not map to centroFlye assembly, Hanging index test, and Breakpoint test

PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline. This pipeline enables nanopore-based variant calling with DeepVariant.

a de novo genome assembler for long reads. Raven is a de novo genome assembler for long uncorrected reads.