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1183 days ago
Five points for bioinformatics software/tools
...ot absolve you of the need to actually read and research the type of analysis that you are doing. This is particularly true in the case of genome assembly and annotation. At the end,...3751 days ago
Dynamic chromosome breakpoints !!!
...yribonucleic acid (DNA) goes through a condensation and decondensation process. This is followed by nuclear envelope dissolution, mitotic spindle assembly, migration of the sister chro...3596 days ago
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 Gopal3954 days ago
Next Generation Sequencing (NGS) Tutorials
...Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI Microbial de novo Assembly for Illumina Data Introductor...3531 days ago
Bioinformatics approach to Boar Taint
...in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file...3833 days ago
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Want to Know which genome assembler rule the world ?
Assemblathon 2: evaluating de novo methods of genome assembly http://www.gigasciencejournal.com/content/2/1/10/abstract http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searchin...3963 days ago
Bio++ : C Language libraries for your biological need
...to many machine-level features that would otherwise require the use of Assembly Language. As Dennis Ritchie...need for a system implementation language efficient enough to displace assembly language, yet sufficiently ab...3991 days ago
Genome Assembly Tools and Software - PART2 !!
...s and it rteturns an improved assembly (more contiguous and more cor...and removes them prior to the assembly. The established software Phr...nbsp;is a method for accurate assembly of a heterogeneous viral popu...o use for your Velvet de novo assembly. It needs two inputs: the est...2729 days ago
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Bioinformatics JRF/SRF position at IARI
...ence in proteomics, genomics and structural biology. Knowledge of programming language, perl and database – HTML, CSS, Java script. NGS sequence assembly and analysis and algorithm de...3575 days ago
Postgraduate Research Associate Bioinformatics / Computational Biology (Reference code: 59)
...beet (Dohm et al., Nature, 2014), a crop plant closely related to quinoa (same family, but different genus). Not yet published is a quinoa genome assembly that we have generated, and w...3240 days ago
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How DNA is Packaged (Advanced)
...CRIPT: In this animation we'll see the remarkable way our DNA is tightly packed up to fit into the nucleus of every cell. The process starts with assembly of a nucleosome, which is for...3920 days ago
Download the genome from NCBI using bash script/command
...cd genome # Look for genome assembly summary and extract the URL...nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"}...nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"}....nih.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"}...2576 days ago
Download the gff files from NCBI using bash script/command
...genome_gff # Look for genome assembly summary and extract the URL...nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"}...nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"}....nih.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"}...2567 days ago
Which of the following programming language is best for a bioinformatics beginner?
...rk and I will like to learn a programming language which is compatible with most bioinformatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and...3574 days ago
3987 days ago
Tags: SPAdes, hybrid, genome, assembly, ONT, Nanopore
2395 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
869 days ago
Comment on "Short-read assembly using Spades !"
...software tool for short-read assembly. Here are the general steps for short-read assembly using SPAdes: Quality co...TQ format. Evaluation of assembly: After running SPAdes, the ne...repeated until a satisfactory assembly is achieved. These are t...459 days ago
Comment on "Short-read assembly using Spades !"
...e assembler) is a popular tool for short-read assembly. It can assemble reads genera...overview of how to use SPAdes for short-read assembly: Install SPAdes: SPAdes...also provides several options for tuning the assembly parameters, such as adjusting...464 days ago