Results for "NCBI Remap"
Bio-Scripts
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.1098 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been re...gp' program is available in the legacy NCBI BLAST package (no longer supported), which is available from the NCBI's FTP site: ftp://ftp.ncbi.nl...f90filt -i uniref90filt #When using NCBI...994 days ago
Command line to download blast database / protein
#download all available nr - protein database as a single file #Database location - NCBI where all databases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/...equences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI...987 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-blast-2.6.0+-x64-linux.tar.gz...xport OMP_NUM_THREADS=??? module load ncbi-...986 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options] Name Typ...R Aminoacid - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA -...T Nucleotide - https://ftp.ncbi....986 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosophila melongaster PacBio assembly cd /genetics/elbers/test/fly2 wget https://ftp.ncbi....962 days ago
Bash command to explore assembly summary genbank !
wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt pip3 install csvkit csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \ | tail -n +2 | tr ";" "\n" \ | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \ | sort | uniq -c | sort -nr812 days ago
Download lumpy skin disease data !
Location https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=880745 The raw genome sequence data from the 2022 outbreak in India is available in the SRA Project PRJNA880745454 days ago
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