1130 days ago
1123 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,...3691 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...3536 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 Gopal3894 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...3471 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...3773 days ago
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3928 days ago
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...3903 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...3931 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...2669 days ago
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3530 days ago
3229 days ago
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...3515 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...3180 days ago
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2976 days ago
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...3860 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"}...2515 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"}...2507 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...3514 days ago
3927 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 GopalTags: Sequencing, assembly, de novo assembly, velvet
3894 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
2475 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...399 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...404 days ago