1211 days ago
1199 days ago
Perl script to run awk inside perl
#!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (remove #! line above if ind...1159 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...tar xzf $a; done #Out of the directory cd .. else echo -e "exists \t blastDB, If not installed sucessfully, delete the folder and re-run it" fi echo -e "\nAll Don...1156 days ago
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt991 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa991 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D957 days ago
Command line to download blast database / protein
...# Database detail / description nr.*tar.gz | Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq #First run this to download wget 'ftp:/...939 days ago
Downloading mmseqs databases !
...- https://cge.cbs.dtu.dk/services/ResFinder - Kalamari Nucleotide yes https://github.com/lskatz/Kalamari #For example, run the following to download and...937 days ago
Installing Covid19 Environment !
...in metagenomic datasets) * BUSCO tools and databases (needed for searching BUSCO genes) -- works in Linux only! To be able to use those, please run quast-download-gridss...919 days ago