Tools to detect synteny blocks regions among multiple genomes
...iuc.edu/labs/lewin/donthu/Synteny_assign/html/), SyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors...2608 days ago
Computer simulation of genetic mechanism !!
...n individual based model intended to simulate datasets under a very broad range of c...simulator for the simulation of case control datasets at SNP markers https://mathge...e replica, differential, non-stranded RNA-Seq datasets. http://useq.sourceforge.net/...2972 days ago
List of popular bioinformatics software/tools
In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.3943 days ago
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Genome Assembly Tools and Software - PART2 !!
...performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference g...computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to p...2683 days ago
Awesome perl frameworks, libraries and software - PART 4
...s a suite of tools for parsing, analyzing, and graphing logs and other datasets. schweikert/postgrey -...amework datameet/india-election-data - To map publicly available datasets related to General Assembly (...2492 days ago
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Useful Publications and Websites for Deep Sequencing Data Analysis
...rror correction of high-throughput sequencing datasets with non-uniform coverage. Me...Geoseq: a tool for dissecting deep-sequencing datasets. Gurtowski et al, BMC Bioinfo...of R and Bioconductor for analysis of genomic datasets, available at R and Bioconduc...3777 days ago
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Structural polymorphism analysis from NGS data
...nformatician will therefore also have to provide researchers with advices on their experimental designs in order to ensure compliance of produced datasets with pipelines requirements....3946 days ago
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Computational Biology in the 21st Century: Making Sense out of Massive Data
...ical data, which will soon outstrip advances in computing power to perform current methods of analysis. Extracting new science from these massive datasets will require not only faster...3899 days ago
Critical to discoveries in bioinformatics
EMBL-EBI distributes datasets worldwide using the Janet network. This biological data enables the discovery of new drugs, new diagnostics and increasingly new agro-chemicals. The...3790 days ago
Installing ggplot2 and its dependencies on Ubuntu !
...-o colorspace.so colorspace.o init.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/colorspace/libs ** R ** data *** moving datasets to lazyload DB ** demo ** i...1547 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 # The number of datasets to subselect from the project. N=5 # Get...1540 days ago
Tryst with a Bioinformatician # Dr Altan Kara
...cs company will be developing effective tools to eliminate manipulated datasets and information that exist in the literature and provide trustworthy clean information/datasets for researchers. How muc...2359 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in output for easy plotting. gcp: K-mer GC Pr...Tags: KAT, K-mer, analysis, toolkit, quality, control, NGS, datasets, genome, assemblies
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Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets
Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Developper: Gaëtan Benoit, PhD, former member of the Genscale team at Inria. Contact: claire dot lemaitre at i...Tags: Simka, SimkaMin, comparative, metagenomics, method, dedicated, NGS, datasets
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Comment on "CovCal: Coverage / Read Count Calculator"
...er of reads that covers each base of the reference genome. Estimating the sequencing coverage is very important when you are simulating datasets. The coverage equation is def...581 days ago
Comment on "ncbi-datasets-cli -- Quickstart: command line tools !"
...(base) [jnarayan@hn1 TOOLS]$ curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd...mat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd...(base) [jnarayan@hn1 TOOLS]$ chmod +x datasets dataformat...878 days ago