Results for "Genome Project"
Bio-Scripts
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f covid19-environment.yml Collect...tructural variants detection) * SILVA 16S rRNA database (needed for reference genome...937 days ago
Bash script to simulate a genome !
...wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0034...ols/BBMap https://sourceforge.net/projects/bbmap/ /genetics/elbers/bb..._upper.diploid.fasta.log.txt # genome size bgzip -@75 -cd GCA_00340...ols/BBMap https://sourceforge.net/projects/bbmap/ /genetics/elbers/bbm...932 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size N (here, N=500), by using the fo...} { print >> file; }' < multi.fasta #Another great solution is genome tools (gt), which you can find here: http://genomet...837 days ago
- #R is a feature rich interpretive programming language or...d extract cd ~/workspace/bin wget https://cran.r-project.org/src/base/R-3/R-3.5.1.tar....lyr", "tidyr", "ggplot2"), repos="http://cran.us.r-project.org")'
837 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome...837 days ago
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in -dbtype nucl -out Next, use megablast from blast+ package to perform all-vs-all blastn of sequences: blastn -query...649 days ago
Genome Scaffolding and gap filling !
scaffolding with ARCS v1.0.3 (−c3, −l,4, −a,0.9, −z500, −m50, −20 000, −e30000, −s90). https://github.com/bcgsc/arcs Next, automated gap filling was performed using Sealer v2.0.1 (−L150, -P10, −k75-115 [step = 10]) https://github.com/bcgsc/abyss/tree/sealer-release634 days ago
Identify genome-wide synteny with LASTZ alignment
#This is the walkstrough how to identifiy genome-wide synteny markers based on LAS.... Step1：Mask the repeat sequences for both genomes and chromosomes. RepeatMa...ps://github.com/yiliao1022/Centromere_synteny_project531 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequ...:RepeatMasker->new(); my $rm_report = $rm->run($genome_...439 days ago
Download lumpy skin disease data !
Location https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=880745 The raw genome sequence data from the 2022 outbreak in India is available in the SRA Project PRJNA880745424 days ago
