Bioinformatics tools for telomere to telomere assembly !
● Merfin – k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Ara...dh)● tama (Transcriptome Annotation by Modular Algorithms) – software des...996 days ago
Protocol for De novo Genome Assembly using Illumina Reads
In this protocol, we address and describe the de novo assembly method for small to medium-sized genomes. What is d...Genome visualisers and editors:Artemis - http://www.sanger.ac.uk/resources/software/art...1208 days ago
Run bash script in Perl program !
BioPerl is a compilation of Perl modules that can be used to build bioinformatics-relate...e, in the development of source codes, standalone software/tools, and algorithms in bioi...commonly favoured over Perl, some bioinformatics software, su...641 days ago
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is collinearity analysis, and the other is based on...is a little troublesome to install, because it depends on a lot of software. wgd depends on the following software BL...1159 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, Ferns B, Goulder P, Nastouli...mp; Salzberg, S. L. Genome Biol. 15, R46 (2014). MUMmer: Versatile and open software for...1051 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 (...881 days ago
List of comparative genomics resources !
3D-GENOMICS -- A Database to Compare Structural and Functional Annotatio...CoCoa -- COefficient of COAncestry software Find information about the a...prokaryotes made easy A web-based software/database system aimed at an i...- Comparative Genomic Hybridization software Vi...681 days ago
Bioinformatics tools to explore SSRs in genomes !
There are several bioinformatics tools that can be used to explore Simple Sequence Repea...ow complexity regions. SciRoKo: SciRoKo is a software tool that can identify SSRs i...QDD: QDD (Quick Detection of Duplication) is a software too...429 days ago
Common methods to discover tandem repeats
Tandem repeats are DNA sequences that are repeated in a contiguous m...Tandem Repeat Finder: Tandem Repeat Finder is a software tool that identifies tandem r...ition. RepeatMasker: RepeatMasker is another software too...427 days ago
Calculate the significance of the difference between two trends
To calculate the significance of the difference between two trends, you can use a statistical t...ific details of each step will depend on the type of test you choose and the software you...422 days ago