Results for "Assembly"
Tags
When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the options: spades.py This produces: SPAdes genome ...Tags: SPAdes, hybrid, genome, assembly, ONT, Nanopore
2351 days ago
Short-read assembly using Spades !
If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina forward reads illumina_R2.fastq.gz: the Illumina reve...Tags: spades, assembly, short, reads, genome, tools
825 days ago
Bioinformatics tools for genome assembly !
There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021: SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as...Tags: bioinformatics, tools, genome, assembly
286 days ago
Mitochondrial genome assembly tools !
Mitochondrial genome assembly tools are specialized software and algorithms designed to accurately reconstruct the mitochondrial genome (mitogenome) from sequencing data, typically obtained through techniques like next-generation sequencing (NGS). The mitochondrial genome is relatively small comp...Tags: Mitochondrial, genome, assembly, tools
242 days ago
Commercial and public next-gen-seq (NGS) software
Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Wind...Tags: Bioinformatics, Computational Biology, NGS, Next generation sequencing, Tools, Software, SNP, Assembly, Pipeline
3519 days ago
Genome Assembly Tools and Software - PART1 !!
The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for your assembly. For the sake of computational me...Tags: Bioinformatics, Genome, NGS, Assembly, Tools, Visualization
2686 days ago
