Results for "assembly"
Tags
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the pa...Tags: LR_Gapcloser, tiling, path-based, gap, closer, long, reads, complete, genome, assembly
1434 days ago
Referee: Genome assembly quality scores
Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality sc...Tags: Referee, Genome, assembly, quality, scores, ngs
1991 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast,...Tags: SKESA, strategic, k-mer, extension, scrupulous, assemblies, genome, assembly
1982 days ago
- MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accele...
Tags: MEGAHIT, ultra-fast, single-node, solution, large, complex, metagenomics, assembly, succinct, de Bruijn, graph
1982 days ago
- Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assemb...
Tags: Genobuntu, software, package, packages, oriented, NGS, assembly, genome
1955 days ago
ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline, called ALLHIC,...Tags: ALLHiC, Phasing, scaffolding, polyploid, genomes, Hi-C, data, assembly
1945 days ago
Versatile genome assembly evaluation with QUAST-LG
QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large ...Tags: Versatile, genome, assembly, evaluation, QUAST-LG
1944 days ago
Genome assembly tutorial "Genome Assembly for short and long reads"
In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know: How to perform basic quality checks on the...Tags: Genome, assembly, tutorial, short, long, reads
1915 days ago
SvABA: Genome-wide detection of structural variants and indels 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, Genome-wide, detection, structural, variants, indels, local, assembly
1913 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file containing both the corrected contigs and the correct, u...Tags: NxRepair, error, correction, denovo, assembly, Nextera, Mate, Pair, Reads
1910 days ago
