Results for "NGS data analysis"
Bio-Scripts
(JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen...ng with flexible solve. Solving environment: failed with repodata fro...1220 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_...ikraken2_v2_8GB_201904_UPDATE/database100mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/database150mers.kmer_distrib mini...p-compressed --paired ../mappings/evol1.sorted.unmapped.R1.fastq.gz ../mappings/evol...1219 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...rc/CMakeFiles/i-visualize.dir/DataSet.cpp.o [ 59%] Building CXX.../CMakeFiles/i-adhore.dir/Settings.cpp.o [ 83%] Building CXX obj...akeFiles/i-visualize.dir/Settings.cpp.o [ 95%] Linking CXX exec.../anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210_201/sca.../anaconda3/envs/wgd/./testset/datasetI...1208 days ago
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_database...1165 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...
1163 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required modules have been...r', 'File::Copy', 'POSIX', 'Tie::File', 'Try::Tiny', 'Data::Du...1160 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.1059 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r...asename.aligned.bam bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/ref...1049 days ago
Tadpole is 250x faster than SPADes assembler !
...file for reads to use as kmer data. in2= Second input file for paired data. extra= Extra files f...ressive error correction settings. Override...rvative error correction settings. Override...ter assemblies for low-depth data, bu...980 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda en...ironment.yml Collecting package metadata (repodata.json): done Solving environm...############# | 100% importlib-metadata-4 | 32 KB | #############...eed to manually update the taxonomy database...928 days ago
