Results for "Statistics and Probability"
Bio-Scripts
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD...1349 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solv...
1227 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::Simple;...been installed in the system and download the mandatory database # BEGIN {...File::Spec::Functions', 'Statistics::Multtest', 'File::Path', 'Statistics::Distributions',...1172 days ago
- #use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Arc...dules have been installed in the system and download the mandatory database # BEGIN {...p', 'File::Spec::Functions', 'Statistics::Multtest', 'File::Path', 'Statistics:...
1170 days ago
Perl script to check modules installed !
#use strict; use warnings; use ExtUtils::Installed; # # First, check if all the required m...'File::Temp', 'File::Spec::Functions', 'Statistics::Multtest', 'File::Path', 'Statistics:...1167 days ago
Tadpole is 250x faster than SPADes assembler !
...ut= mode=correct Extension and correction may be done simultaneousl...Ignore kmers with overall probability of correctness below...xtend sequences to be longer, and optionally...kmer-counting, and again prior to correction. Output...988 days ago
- blastpgp arguments: -d Database [String] default = nr -i Query F...ities, 5 = query-anchored no identities and blunt ends, 6 = flat query-anchored, no identities and blunt ends, 7 = XML Blast ou...default = F -t Use composition based statistics...
962 days ago
Perl script to parse blast results and plot basic stats !
#!/usr/bin/perl use strict; use warnings; use List::Util qw(sum); # Usage: ./parse_blast...----------------------\n"; } # Calculate additional sta..._stats(\@blast_entries, 'BITSCORE'); # Print summary statistics...106 days ago
Perl script to calculate the basic stats of the assembled genome !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Input fi...a'); # Variables for computing statistics my $total_length = 0; my $n...engths; # Calculate additional statistics my $min_contig_length = $con...ut_file); # Print the computed statistics and informa...106 days ago
Python script for basic stats of the assembled genome !
from Bio import SeqIO import statistics # Input file containing the ge...sta' # Variables for computing statistics total_length = 0 num_contig...e=True) # Calculate additional statistics min_contig_length = min(cont...ntage, 2) # Print the computed statistics and informa...106 days ago
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