Download the genome from NCBI using bash script/command
...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...2531 days ago
Download the gff files from NCBI using bash script/command
...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...l 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary...s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...2522 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna path=/home/urbe/Tools/SATSUMA/satsuma-code-0 for f in...2331 days ago
Download genomes in batch from NCBI
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file2262 days ago
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Pack a perl program with their dependencies on Ubuntu !
...assemblies of hundreds of microbial genomes and highly contiguous reconstruct...of many dozens of plant and animal genomes, enabling new insights into evolu...ere: https://www.lazoi.com/Home Comparative Genomics !!This group is dedicated to Comparative genomics ... Dramatic res...1510 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosophila melongaste...io assembly cd /genetics/elbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_00340...917 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 -nr767 days ago