To convert just one specific read group to fastq
...SRR numbers. cat runinfo.txt | cut -f 1 -d , | grep SRR | head -$N > selected.txt # Store the data in the reads folder. mkdir -p reads # Download the SRR data for each cat se...1540 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker dock...aded. jit@jit-HP-Pro-3335-MT:~/Downloads$ curl -fsSL https://get.dock...er.sh jit@jit-HP-Pro-3335-MT:~/Downloads$ chmod 777 get-docker.sh...tion. jit@jit-HP-Pro-3335-MT:~/Downloads$ docker Usage: docker [OP...1511 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...1212 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioinformatics-psb-ugent-be.translate.goog/webtools/i-adhore/licensing/ #Follow these s...1201 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://ww...1180 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...been installed in the system and download the mandatory database # BE...ash script else here print "\nDownloading third party database for A...ttps://www.arb-silva.de/no_cache/download/archive/release_138_1/Exports...(get("$content"))) { print "Download started"; } if [ ! -d...1158 days ago
1156 days ago
Command line to download blast database / protein
#download all available nr - protein database as a single file #Database location -...from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq #First run this to download wget 'ftp://ftp.ncbi.nlm.nih...941 days ago
Download desire version of Blast software !
#Create a directory and wget it wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz #unpacking blast tar -zxvf ncbi-bl...940 days ago
Downloading mmseqs databases !
...tps://github.com/lskatz/Kalamari #For example, run the following to download and setup the Swiss-Prot at t...olumn above, all necessary files to use it as a valid seqTaxDB will be downloaded and prepared by the databas...940 days ago