Commands to install conda in Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp jit@jit-HP-Pro-3335-MT:~/Downloads$ cd jittmp/ jit@jit-HP-Pro-3335-MT:~/Downloads/jittmp$ curl -O https://repo.anacon...1510 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' input.fasta > output.fasta #R...1356 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_201904.tgz % Total % Received % Xferd Average Speed Time Time...1213 days ago
Steps to install Conda on Linux !
Download the installer: Miniconda installer for Linux. ( https://docs.conda.io/en/latest/miniconda.html#linux-installers ) Anaconda installer for Linux. ( https://www...1181 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::Extract; # # First, check if all the required modules have been installed in the sy...1159 days ago
1157 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required modules have been installed in the system # BEGIN { my @import_modu...1154 days ago
995 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 interleaved reads=100k length=250 mininsert=400 m...988 days ago
Tadpole is 250x faster than SPADes assembler !
...roduce substantially better assemblies for low-depth data, but they are very slow for large metagenomes. Overlap parameters (for overlapping paired-end reads only): merge=f...974 days ago