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 (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same s...Tags: HASLR, tool, rapid, genome, assembly, long, sequencing, reads
1545 days ago
3D de novo assembly (3D DNA) pipeline
For 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 the pipeline and to reproduce the Hs2-HiC and the AaegL4 genomes reported in (...Tags: 3D, de novo, assembly, 3D, DNA, pipeline
1543 days ago
MEC: Contig Misassembly Correction
MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the stati...Tags: MEC, Contig, Misassembly, Correction, assembly
1540 days ago
Tags: data, reads, free, tree, assembly
1538 days ago
Tags: download, database, ncbi, ftp, genome, dna, reads, genome, assembly, files, ucsc
1533 days ago
BlobToolKit: A toolkit for genome assembly QC
Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible filtering. BlobToolKit is comprised of four component...Tags: BlobToolKit, toolkit, genome, assembly, QC
1524 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (wi...Tags: SvABA, Structural, variation, indel, detection, local, assembly
1506 days ago
JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wikiTags: JCVI, Python, utility, libraries, genome, assembly, annotation, comparative, genomics, synteny, plots
1499 days ago
Tags: Corona, virus, China, Resources, CoVID, covid, china, genome, assembly, dna, rna, sequences, evolution, study, comparative, genomics
1448 days ago
Tags: HiCanu, accurate, assembly, segmental, duplications, satellites, allelic, variants, high-fidelity, long, reads
1488 days ago