Results for "structural and sequence variation"
Bio-Scripts
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env cr...Solving environment: done Downloading and Extracting Packages sqlite-3...e does not include: * GRIDSS (needed for structur...n in metagenomic datasets) * BUSCO tools and datab...943 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/resources/pangolin/usage.html (base) [jnarayan@..._for_Cova_all_samples_combined.fa ** Running sequence QC ** Number of sequences detected: 320 Total passing...ns warnings.warn( processing block of 293 sequences...907 days ago
bash script to extract sequence by ids !
Use a Perl one-liner, grep and seqtk subseq to extract the desired fasta sequences: # Create test input: cat > in.fasta BGI_novel_T016313 Soly...t ids_gene_ids.tsv | cut -f1 > ids.selected.txt # Extract fasta sequence...843 days ago
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in -dbtype nucl -out Next, use megabl...om blast+ package to perform all-vs-all blastn of sequences: blastn -query -db -outfmt...airwise ANI by combining local alignments between sequence...655 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::...$genome_file = "genome.fasta"; # read genome sequence my $seqio = Bio::SeqIO-...my $rm_end = $rm_result->end(); my $rm_strand = $rm_result->strand();...445 days ago
Raku script to find palindrome in genomes !
sub is-palindrome(Str $str) returns Bool { $str.=uc; # convert to uppercase...usage my $dna = "GGATCCATGGCCTAGG"; # example DNA sequence find-palindromes($dna, 3, 8); # find palindromes with length between 3 and 8444 days ago
Perl script for chi-squared test !
#!/usr/bin/perl # # chidi.pl # # A script to perform a chi...##################### # Read sequence file 1 ################...FILE); # loop through each sequence in file 1 while(my $entry =...p through sequence, take 2 bp and increment the hash counter forea...431 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 PRJNA880745430 days ago
Raku script to calculate GC content !
sub calculate-gc-content(Str $sequence) { my $gc-count = $sequence.comb(//).elems; my $total-bases = $sequence.chars; return $gc-count / $total-bases * 100; }...GCGCGCGCGC"; my $gc_content = calculate-gc-content($dna_sequence)...131 days ago
Raku script to find SSRs in fastq file !
sub find-ssrs(Str $sequence) { my @ssrs; for 2..$sequence.chars -> $min-repeats { for $sequence.chars...$min-repeats -> $max-...-length, sequence => $repeat }...g the next two lines (comment and quality lines) $fh.readli...131 days ago
