Results for "benchmarking and designing tools"
Bio-Scripts
Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it...i-ADHoRe #Creat the conda ENV and install its deps #Follow the...ne-any.whl (176 kB) Collecting pandas==0.24.1 Downloading pand...it-learn, PyYAML, python-utils, pandas, pa...RANTY; This is free software, and y...1203 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...ir/levelTwo.cpp.o /home/urbe/Tools/i-a...to a region of size between 0 and 6 [-Wformat-overflow=] string...ir/parallel.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter...sprintf_chk’ output between 8 and 26 bytes into a destination of...I/vvi_lists_030210_201/chr11_random.lst -- Installing: /home/urb...1203 days ago
- ...bpcrecpp0v5 libpng-dev libpng-tools lib...nic-updates/main amd64 icu-devtools amd64 60.2-3ubuntu3.1 [179 kB...nic-updates/main amd64 libpng-tools amd64 1.6.34-1ubuntu0.18.04.2...ing database ... 202932 files and directories currently installed...sly unselected package libpng-tools. Preparing to unpack .../081...
1054 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.1053 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_BBM...java -ea -Xmx162129m -cp /home/urbe/Tools/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa ou...sert=600 gaussian Executing align2.RandomReads3 [build=1, ref=mixed.fa,...989 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$...ironment: done Downloading and Extracting Packages sqlite-3...############### | 100% setuptools-58....################# | 100% bedtools-2.30.0 | 17.9 MB | ###...omic datasets) * BUSCO tools and databases (needed for searching...923 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size N (here....fasta #Another great solution is genome tools (gt), which you can find here: http://genometools.org/, which has the following simple command: gt splitfasta -numfiles 10...822 days ago
- $ sudo apt install art-nextgen-simulation-tools [sudo] password for neelam...newly installed, 0 to remove and 1 not upgraded. Need to get 2,...amd64 art-nextgen-simulation-tools amd64 20160605+dfsg-4 [1,681...ing database ... 178334 files and directories currently installed...
664 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file...(); # run RepeatMasker my $rm = Bio::Tools::Ru..._end = $rm_result->end(); my $rm_strand = $rm_result->strand(); if ($rm_class eq...424 days ago
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