Computer simulation of genetic mechanism !!
Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyz...3026 days ago
2581 days ago
BBTools for bioinformatician !
BBMap.sh Mapping Nanopore reads BBMap.sh has a length cap of 6kbp. Reads longer than this will be broken into 6kbp pieces and mapped independently. Code: $ ma...2321 days ago
Basic command-line to run BLAST
The goal of this tutorial is to run you through a demonstration of the command line, which you may not have seen or used much before. All of the commands below...2295 days ago
2184 days ago
Converting a VCF into a FASTA given some reference !
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528) This script has been modified b...2167 days ago
CANU genome assembly parameters !
Choose the appropriate parameters to run Canu and run it. The assembly will take about an hour. You can use two cores (parameter -maxThreads=2) and you would like...1996 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 de novo genome assembly?The method of taking a large n...1255 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 the Ks distribution map. Among them, Ks is defined as the avera...1206 days ago