Plot the density of genes in R
...ll and load it if("ggplot2" %in% rownames(installed.packages())){ library(ggplot2) } else { install.packages("ggplot2") library(ggplot2) } # import a...2331 days ago
2311 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_file2310 days ago
2299 days ago
Perl script to remove fasta sequences in multifasta file with certain length threshold
#!/usr/bin/perl use strict; use warnings; my $minlen = shift or die "Error: `minlen` parameter not provided\n"; { local $/=">"; while() { chomp...2298 days ago
Perl script to convert fastq to fasta file
#!/usr/bin/env perl use strict; use warnings; use Bio::Factory::EMBOSS; my $usage = "perl $0 in.fq out.fa"; my $infile = shi...ie $usage; my $outfile = shift or die $usage; my $factory = Bio::Factory::EMBOSS->new; my...2298 days ago
Plot custom gene density with R
library(karyoploteR) pp2297 days ago
Estimate Genome Size with Jellyfish and R
...nome_estimation/sample_read_2.fastq #-t -treads=unit32 Number of treads to be used in the run. eg: 1,2,3,....-output=string Output file name #--min-quality-char Base quality value. Version 2.2...2293 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2286 days ago
Perl script to find missing and move to desire folder
#!/usr/bin/perl -w use strict; use warnings; open(my $ids, "2286 days ago