Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosophila melongas...lbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_0034...174v1_genomic.fna_upper.diploid.fasta.log.txt # genome...938 days ago
887 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...843 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...843 days ago
Multiline fasta to single line fasta !
perl -pe '$. > 1 and /^>/ ? print "\n" : chomp' in.fasta > out.fasta815 days ago
Bash script to convert multiline fasta to single line fasta !
#file.fa is multiline fasta awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa786 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...655 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-release640 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...537 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_...445 days ago