Results for "assembly"


  • Comparison of Short Read De Novo Alignment Algorithms

    Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms  Author: Nikhil Gopal

    Tags: Sequencing, assembly, de novo assembly, velvet

    1649 days ago

  • Omega2: metagenome assembly pipeline

    Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph and then merged to contigs and scaffolds using m...

    Tags: Omega2, metagenome, assembly, pipeline

    230 days ago

  • Unicycler: Hybrid assembly pipeline for bacterial genomes

    Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible asse...

    Tags: Unicycler, Hybrid, assembly, pipeline, bacterial, genomes

    107 days ago

  • ONT assembly and Illumina polishing pipeline

    This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem. Perform correction of contigs using p...

    Tags: ONT, assembly, Illumina, polishing, pipeline

    94 days ago

  • coursera genome assembly tutorial

    Solutions to Coursera Genome Sequencing (Bioinformatics II)

    Tags: coursera, genome, assembly, tutorial

    92 days ago

  • miniasm: very fast OLC-based de novo assembler for noisy long reads

    Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. I...

    Tags: Ultrafast, de novo, assembly, long, noisy, reads, consensus

    90 days ago

  • dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements

    dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not requ...

    Tags: dnaPipeTE, de-novo, assembly, annotation, Pipeline, Transposable, Elements

    85 days ago

  • COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

    An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, whic...

    Tags: COPE, accurate, k-mer, pair-end, reads, connection, tool, genome, assembly

    82 days ago

  • MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)

    MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but...

    Tags: MashMap, fast, approximate, software, mapping, long, reads, PacBio, ONT, assembly, reference, genome(s)

    75 days ago

  • Ra assembler - a de novo DNA assembler for third generation sequencing data

    Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in development since 2014 in the form of several separa...

    Tags: Ra, assembler, de novo, DNA, assembler, third, generation, sequencing, assembly

    60 days ago