Results for "assembly"

Tags

  • 3d-dna: 3D de novo assembly (3D DNA) pipeline

    This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise noted, all terminology below is consistent with t...

    Tags: 3D, de novo, assembly, 3D, DNA, pipeline

    2282 days ago

  • RGFA: powerful and convenient handling of assembly graphs

    RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is ...

    Tags: RGFA, powerful, convenient, handling, assembly, graphs, GFA

    1529 days ago

  • Genome assembly stats plotting

    A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig Scaffold/contig N50 and N90Assembly base composition, in particular percentage GC and percentage Ns CEGMA complet...

    Tags: Genome, assembly, stats, plotting

    2220 days ago

  • AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

    AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --...

    Tags: AlignGraph, algorithm, secondary, de novo, genome, assembly, guided, references

    2172 days ago

  • ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

    ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.  Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

    Tags: ALPACA, hybrid, strategy, assembly, genomic, DNA, shotgun, sequencing, reads

    2159 days ago

  • MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

    MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for e...

    Tags: MECAT, fast mapping, error correction, de novo, assembly, genome, single-molecule, sequencing, reads, Tools

    2148 days ago

  • HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

    HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccura...

    Tags: HapCUT2, robust, accurate, haplotype, assembly, diverse, sequencing, technologies

    2144 days ago

  • EAGLER: a scaffolding tool for long reads.

    EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nano...

    Tags: EAGLER, scaffolding, tool, long, reads, genome, assembly

    2124 days ago

  • PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach

    PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct contig, PERGA uses paired-end reads and differen...

    Tags: PERGA, Paired-End, Read, Guided, De Novo, Assembler, Extending, Contigs, SVM, Look, Ahead, Approach, assembly

    2123 days ago

  • Cerulean: A hybrid assembly using high throughput short and long reads

    Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in Deshpande, V., Fung, E. D., Pham, S., & Bafna, V. (...

    Tags: Cerulean, hybrid, assembly, short, long, reads, pacbio, nanopore

    2123 days ago