LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads. https://ac...Tags: LoReTTA, user-friendly, tool, assembly, viral, genomes, PacBio, sequence, data
1044 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. https://academic.oup.com/nar/article/47/11/e63/537...Tags: MitoZ, toolkit, animal, mitochondrial, genome, assembly, annotation, visualization
883 days ago
odgi: optimized dynamic genome/graph implementation
odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently compute and transform pangenomes with mini...Tags: odgi, optimized, dynamic, genome, graph, implementation, genome, assembly, graph
820 days ago
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the read alignment and variant caller’s interna...Tags: Merfin, improved, variant, filtering, assembly, evaluation, polishing, k-mer, validation
759 days ago
auN: a new metric to measure assembly contiguity
Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A longer N50 indicates better contiguity. We can si...Tags: auN, new, metric, measure, assembly, contiguity
639 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-yTags: MitoHiFi, python, pipeline, mitochondrial, genome, assembly, PacBio, fidelity, reads
240 days ago
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior sp...Tags: MIKE, ultrafast, assembly, alignment-free, approach, phylogenetic, tree, construction
24 days ago
Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, MAKER, Genome, Annotation, Pipeline, NGS, Assembly
3006 days ago
Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, BUSCO, Genome, Annotation, Pipeline, NGS, Assembly, Orthologs
3006 days ago
Tags: Bioinformatics, Computational Biology, Education, Cancer, Research, RATT, Genome, Annotation, Pipeline, NGS, Assembly
3006 days ago