NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. Af...1576 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, a...1557 days ago
SLR-superscaffolder: 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. Here is an illustration of this pipeline:1536 days ago
Juicebox: Visualization and analysis software for Hi-C data
...s below pertain primarily to usage of command line tools and the Juicebox jar files. Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juiceb...1529 days ago
1343 days ago
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works wit...ry/alternate assemblies of quality competitive with the best assemblers. It also introduces a new g...1222 days ago
Genome assembly training tutorial at Galaxy !
In this tutorial we assemble and annotate the genome of E. coli strain C-1. This strain is routinely used in experimental evolution studies involving bacteriophages. For instance,...1219 days ago
244 days ago
Peregrine & SHIMMER Genome Assembly Toolkit
Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads...hout quadratic comparisions used in other OLC assemblers.865 days ago
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y237 days ago