Results for "B"
Bio-Scripts
Conda command to install checkV
...------|----------------- boost-1.68.0 |py3...758 KB bioconda importlib-metadata-4.2.0 | py36h5fa...python-1.79-py36h8f6f2f9_0 boost conda-forge/...kcounter-0.1.1 | 871 KB | ########################...698 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 -qu...ed up the search at the cost of sensitivity: blastn -query -db -outfmt '6...698 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
- (jitENV) [jnarayan@hn1 preetiDATA]$ blastn -task blastn -query list_flank_0.fa -subject ../monkeypoxDATA_07_06_22/JIT_gisaid_pox_2022_09_06_07.fasta -evalue 20000000 -word_size 5 -num_threads 4 -outfmt 6 -out blastn_0.txt -qcov_hsp_perc 100 -perc_identity 100 -max_target_seqs 10000
654 days ago
Extract the mapped and unmapped reads !
...CESSORS=20 #Single_End_Layout: samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam #Paired_End_Layout samt...652 days ago
Identify genome-wide synteny with LASTZ alignment
...dentifiy genome-wide synteny markers based on LASTZ alignment. Step1：Mask the repeat sequences for both genomes and chromosomes....-pa 40 -nolow -norna -gff -xmall -lib custom.TE.lib_for_rice.fa AAC...1 -o syn.final.out @ https://github.com/yiliao1022/Centromere_syn...579 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker;...ad genome sequence my $seqio = Bio::SeqIO->new(-file => $genom...# run RepeatMasker my $rm = Bio::Tools::Run::RepeatMasker->...ted") { my $rm_seq = substr($seq, $rm_start-1, $rm_end...487 days ago
Perl script to find edit distance between two sequences !
#!/usr/bin/perl use strict; use warnings; sub edit_distance { my ($s1, $s2) = @_; my $len1 = length($s1); my $len2 = length($s2); my @dp; for (my $i = 0; $i487 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 space...rn $str eq $str.flip; } sub find-palindromes(Str $dna, In...find palindromes with length between 3 and 8...487 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data480 days ago
