Results for "Assembly"
Tags
wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. ./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo p...Tags: wtdbg2, fuzzy, Bruijn, graph, approach, long, noisy, reads, assembly
1905 days ago
SDA: Long-read sequence and assembly of segmental duplications
Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs. ht...Tags: SDA, Long-read, sequence, assembly, segmental, duplications
1876 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes...Tags: Flye, Fast, accurate, de novo, assembler, single, molecule, sequencing, reads, ngs, assembly
1847 days ago
GMASS: a novel measure for genomeassembly structural similarity
The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo assemblers. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2710-zTags: GMASS, novel, measure, genome, assembly, structural, similarity
1835 days ago
How to get better alignment results of PAcBio data?
HI! I am Nadia. I am trying to align PAcBio data (data from third generation sequencer) using bwa mem. I am getting very less number of aligned reads in SAM file having coverage of less than 10X. I tried to use minimap2 as well for alignment but again the quality of sam file isn,t good. I am get...Tags: PacBio, genomic data, NGS, assembly, Arabidopsis data
1798 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range o...Tags: TRITEX, sequence, assembly, pipeline, Triticeae, genomes
1708 days ago
- CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).
Tags: CONTIGuator, python, assembly, bacteria, structure
1663 days ago
