Results for "data visualization"
Bio-Scripts
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::S...em and download the mandatory database # BEGIN { my @impo...ile', 'Try::Tiny', 'Data::Dumper', 'File::Basenam...nt "\nDownloading third party database for Alienomics\n"; #In....arb-silva.de/fileadmin/silva_databases/rel...1173 days ago
- #use strict; use warnings; use ExtUtils::Installed; use LWP::Simple;...the system and download the mandatory database # BEGIN { my @impo...'Tie::File', 'Try::Tiny', 'Data::Dumper', 'File::Basenam...e print "\nDownloading third party database for...
1171 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required modules have been...', 'File::Copy', 'POSIX', 'Tie::File', 'Try::Tiny', 'Data::Dumper'...1168 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.1067 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r...sename.aligned.bam bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/ref_geno...1057 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh Wri...rimary input file for reads to use as kmer data. in2= Second input file for paired data. extra= Extra files f...tantially better assemblies for low-depth data, but the...988 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda e...ronment.yml Collecting package metadata (repodata.json): done Solving environm...############ | 100% importlib-metadata-4 | 32 KB | #############...ed to manually update the taxonomy databases bef...936 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/resources/pangolin/usage.html (base...The query file is:/home/jnarayan/RF_DATA/FASTA/Input_for_Cova_all_samp...tected: 320 Total passing QC: 293 Data files found: Trained model:...ut file written to: /home/jnarayan/RF_DATA/FASTA/li...900 days ago
Installing SEVA environment in Conda !
(base) [jnarayan@hn1 SEVA_codes_and_files]$ conda env create -f SEVA.yaml Collecting package metadata (repodata.json): done Solving environm...##################################### | 100% r-data.table-1....850 days ago
Install StringTie on ubuntu / Linux !
#StringTie is a software program to perform transcript assembly and quantification of RNAseq data. The binary distributions are available so to install we can just download this distribution and extract...836 days ago
