Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it is slightly troublesome to install, because it #depends on a lot of software. wgd depends on the foll...1204 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...sb-ugent-be.translate.goog/webtools/i-adhore/licensing/ #Follo...e been written to: /home/urbe/Tools/i-adhore-3.0.01/build (wgd)...ir/levelTwo.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter...ir/parallel.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter...1204 days ago
1055 days ago
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1055 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired int...rt=400 maxinsert=600 gaussian java -ea -Xmx162129m -cp /home/urbe/Tools/bbmap/current/ align2.RandomR...991 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ c...#################################### | 100% setuptools-58.2.0 | 1008 KB | #####...###################################### | 100% bedtools-2.30.0 | 17.9 MB | ###...924 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size N (here,...t >> file; }' < multi.fasta #Another great solution is genome tools (gt), which you can find here: http://genometools.org/, which has the following...824 days ago
665 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $ge...eqobj->seq(); # run RepeatMasker my $rm = Bio::Tools::Run::RepeatMasker->new(); m...426 days ago