Results for "Assembly"
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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
- 2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science disse...
Tags: Corona, virus, China, Resources, CoVID, covid, china, genome, assembly, dna, rna, sequences, evolution, study, comparative, genomics
1448 days ago
- HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More at https://www.biorxiv.org/content/10.1101/2020.03.14.992248v3
Tags: HiCanu, accurate, assembly, segmental, duplications, satellites, allelic, variants, high-fidelity, long, reads
1489 days ago
RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.Tags: RefKA, fast, efficient, long-read, genome, assembly, approach, large, complex, genomes
1454 days ago
HASLR: a hybrid assembler which uses both second and third generation sequencing reads
HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to othe...Tags: HASLR, hybrid, assembler, third, generation, sequencing, reads, illumina, pacbio, ont, assembly, genome
1451 days ago
Sample bandage input file for visual analysis
Sample bandage input file for visual analysis ...Tags: bandage, assembly, genome, visual, analysis, file, input
1204 days ago
Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library. Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for assembly. Supernova should be run using 38-56x ...Tags: Supernova, phased, whole-genome, de novo, assembly, Chromium-prepared, library
1424 days ago
