Rename the screen name in Linux !
screen -S 22798.pts-5.hn1 -X sessionname node33_COMPUTE767 days ago
726 days ago
Conda command to install checkV
...e/linux-64::boost-cpp-1.68.0-h11c811c_1000 checkv bioconda/noarch::checkv-1.0.1-pyhdfd78af_...linux-64::kcounter-0.1.1-py36h91eb985_1 more-itertools conda-forge/noarch::more-itertools-8.13.0-py...697 days ago
Script to rapid genome clustering based on pairwise ANI
...last+ package to perform all-vs-all blastn of sequences: blastn -query -db -outfmt '6 std qlen slen' -max_target_seqs 10000 -o -num_threads 32 Note: using the -perc_identity f...697 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-release682 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. RepeatMasker -pa 40 -nolow -norna -gff -xmall -lib custom.TE...579 days ago
Perl script to find inverted repeats !
...ings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome se...= Bio::Tools::Run::RepeatMasker->new(); my $rm_report = $rm->run($genome_file); # parse RepeatMas...487 days ago
Raku script to find palindrome in genomes !
sub is-palindrome(Str $str) returns Bool { $str.=uc; # convert to uppercase $str.=subst:g/\s+//; # remove any spaces return $str eq $str.flip; } su...486 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data480 days ago
54 days ago