Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f...ed for structural variants detection) * SILVA 16S rRNA database (needed for reference genome detection in metagenomic data...937 days ago
Bash script to simulate a genome !
...https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0034017...er.diploid.fasta.log.txt # genome size bgzip -@75 -cd GCA_0034017...haplotype from the "diploid" reference bgzip -@75 -dc GCA_003401...ype0.fasta.gz # make reference for randomreads.sh # rand...931 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size N (he...} { print >> file; }' < multi.fasta #Another great solution is genome tools (gt), which you can find here: http://genometools.org/, which has the foll...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 Institute at Washington Unive...837 days ago
BBmap the reads with all alignments !
bbmap.sh in=../reference/reference.numbered.fa ambig=all vslow perfectmode maxsites=100000 out=fetch_Ids_for_barcode.sam832 days ago
805 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 LASTZ alignment. Step1:Mask the repeat sequences for both genomes and chromosomes. RepeatMa...531 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::...eqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequ...:RepeatMasker->new(); my $rm_report = $rm->run($genome_file); # parse RepeatMaske...439 days ago