NextDenovo: string graph-based de novo assembler for TGS long reads
...S long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate is a...1610 days ago
1601 days ago
MGSE: Mapping-based Genome Size Estimation
...n genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script construct_cov_fil...1598 days ago
De novo Genome Assembly for Illumina Data
...uction In this protocol we discuss and outline the process of de novo assembly for small to medium sized genomes. https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/1595 days ago
GfaViz: flexible and interactive visualization of GFA sequence graphs
GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this re...1592 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
...ased toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (...1591 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical for large error prone genomes which makes the assembly process produce an excessive...1587 days ago
HASLR: a tool for rapid genome assembly of long sequencing 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 (suc...1584 days ago
3D de novo assembly (3D DNA) pipeline
...a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly. For the original version of...1581 days ago
Musket - a multistage k-mer spectrum based corrector
...duces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket...1579 days ago