Protocol for De novo Genome Assembly using Illumina Reads
In this protocol, we address and describe the de novo assembly method for small to me...ge Genome visualisers and editors:Artemis - http://www.sanger.ac.uk/resources/software/artemis/IGV - http://www.broa...1244 days ago
Run bash script in Perl program !
BioPerl is a compilation of Perl modules that can be used...le, in the development of source codes, standalone software/tools, and algorithms in bioi...s commonly favoured over Perl, some bioinformatics software, such as the standalone versi...676 days ago
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analys...t is a little troublesome to install, because it depends on a lot of software. wgd depends on the following software BLASTMCLMUSCLE/MAFFT/PRANKPA...1195 days ago
Frequently used bioinformatics tools for viral genome analysis !
IVA: accurate de novo assembly of RNA virus genomes. Hunt M, Gall A, Ong SH, Brener J...& Salzberg, S. L. Genome Biol. 15, R46 (2014). MUMmer: Versatile and open software for comparing large genomes....1086 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment...916 days ago
List of comparative genomics resources !
3D-GENOMICS -- A Database to Compare Stru...CoCoa -- COefficient of COAncestry software Find information about the a...f prokaryotes made easy A web-based software/database system aimed at an i...-- Comparative Genomic Hybridization software Visualize and explore compar...716 days ago
Bioinformatics tools to explore SSRs in genomes !
There are several bioinformatics tools that can be used t...low complexity regions. SciRoKo: SciRoKo is a software tool that can identify SSRs i...QDD: QDD (Quick Detection of Duplication) is a software tool that can identify SSRs i...464 days ago
Common methods to discover tandem repeats
Tandem repeats are DNA sequences that...Tandem Repeat Finder: Tandem Repeat Finder is a software tool that identifies tandem r...sition. RepeatMasker: RepeatMasker is another software tool that can identify tandem...463 days ago
Calculate the significance of the difference between two trends
To calculate the significance of the difference between two trend...ecific details of each step will depend on the type of test you choose and the software you use to perform the analys...457 days ago
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