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Bio-Scripts
Command line to download blast database / protein
...abases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ # Database detail / description nr.*tar.gz | Non-redundant protein sequences...1002 days ago
Download desire version of Blast software !
...acking blast tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz #Slurm template #!/bin/bash #SBATCH --partition=longjobs #SBATCH --nodes=1 #SBATCH --ntasks-per-node=32 #SBATCH --time=1:00:00...1001 days ago
Downloading mmseqs databases !
...Type Taxonomy Url - UniRef100 Aminoacid yes https://www.uni...iref - UniRef50 Aminoacid yes https://www.uni...otkb - UniProtKB/Swiss-Prot Aminoacid yes https://uniprot.../a-new-pfam-b-is-released - eggNOG Profile...1001 days ago
- ...1 \ seed=1 \ ref=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz....sh build=1 \ ref=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz...ow=t seed=1 \ ref=GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz...
987 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f covid19-envir...d. You still need to manually update the taxonomy databases before Krona can...c reports. The update script is ktUpdateTaxonomy.sh. The default location f...982 days ago
Bash script to simulate a genome !
...GCA_003401745.1_ASM340174v1_genomic.fna.gz | \ bgzip -@75 > G...GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz...GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz...GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz...977 days ago
- ...character which is used to divide fields on the input line. The default is “white space”, meaning space and tab characters. FS can be reassigned to another character (typically in B...
954 days ago
Extract fasta sequences with ids in another file !
#Ids are in test.txt - one ids per line #sequences are in test.fa grep -w -A 2 -f test.txt test.fa --no-group-separator # seqtk seqtk subseq test.fa test.txt #faSomeRecods faSomeRecords in.fa listFile out.fa # seqkit seqkit grep -n -f list.txt sequences.fas > newfile2.fas948 days ago
- Lenovo-ideapad-320-15ISK:~/VANSH$ conda update -n base conda Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan #...
921 days ago
Extract the sequences with IDs !
#sed -i 's/\_/ /g' Delta_seqID_from_lineage_report.txt seqtk subseq genomic.fna Delta_seqID_from_lineage_report.txt > Delta.fasta #Split the fasta in 11 equal sequences subsets pyfasta split -n 11 Delta.fasta910 days ago
