Download the genome from NCBI using bash script/command
...curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary...-r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary...-r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...2485 days ago
Download the gff files from NCBI using bash script/command
...curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary...-r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary...-r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_geno...2476 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...2284 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_file2216 days ago
2079 days ago
Pack a perl program with their dependencies on Ubuntu !
...to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into e...1464 days ago
Bash script to simulate a genome !
...com/chhylp123/hifiasm/issues/33 # Use Drosophila melongaster PacBio assembly cd /genetics/elbers/test/fly2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_00340...871 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 -nr721 days ago
Identify genome-wide synteny with LASTZ alignment
#This is the walkstrough how to identifiy genome-wide synteny markers based on LASTZ alignment. Step1:Mask the repeat sequences for both genomes and chromosomes. RepeatMasker -p...470 days ago
Raku script to find palindrome in genomes !
sub is-palindrome(Str $str) returns Bool { $str.=uc; # convert to uppercase $str.=subst:g/\s+//; # remove any spaces return $str eq $str.flip; } sub...378 days ago