Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloa...r-correct reads. Tadpole has no upper bound for kmer length, but some values are not supported. Specifically, it...minextension=2 (mine) Do not keep contigs that did not ex...Remove reads that cannot be used for assembly....1035 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 +D1021 days ago
1020 days ago
Oneliner to convert lower-case to sequence masked with Ns
perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna awk '{if(/^[^>]/)gsub(/[a-z]/,"N");print $0}' genomic.fna > genomic.N-masked.fna1009 days ago
Perl script for Smith-Waterman Algorithm
...letters that mismatch my $GAP = -1; # -1 for any gap # initialization my @matrix; $matrix[0][0]{score} = 0; $matrix[0][0]{pointer} = "none"; for(my $j = 1; $j...1009 days ago
1009 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced by the 'psiblast' program. The 'blastpgp' program is available in the legacy NCBI BLAST package (no longer supported), which is a...1009 days ago
Inreractive SCP / File transfer !
...using scp" #next line check if entered value is not null, and if null it will re...loop done #next line check if entered value is not null, and if null it will re...next line check if entered value is null, and If not null it will reask user to e...1009 days ago
1008 days ago
Get the Linux system information !
...a menu driven system information program DIALOG_CANCEL=1 DIALOG_ESC=255 HEIGHT=0 WIDTH=0 display_result() { dialog --title "$1" \ --no-collapse \ --msgbox "$re...1007 days ago