Results for "long reads"
Bio-Scripts
# To follow these instructions, we'll assume your system admins have already installed these essentials: # Debian...a Statistics::Lite Tie::Autotie Tie::IxHash Log::Log4perl FindBin::Real Getopt::Long...2141 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::...tries => 5, help => undef ); Getopt::Long:...2912 days ago
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2868 days ago
- #! /usr/local/bin/perl5.8.3 -w ### ### Script Name : calcN50.pl ### Description : This script calculates the...r of sequences >= this value is sent to STDOUT ### use strict; use Getopt::Long;...
2701 days ago
- #!/usr/local/bin/perl -w # NOTE: YOU MUST CHANGE THE LINE ABOVE TO POINT TO # THE FULL PATH OF THE PERL EXECUTAB...R "have to install DB_File version 1.814.\n\n"; } } } use Getopt::Long;...
2690 days ago
Genetic Algorithms demonstration with word DNA in Perl
#!/usr/bin/perl -w # GA demonstration with word DNA (512 bits) use strict; use Data...th 0 fitness my $max_entry_length = 20; # longest word we accept # you ca...'s OK) # increment the fitness depending on how long...2368 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::U...cumentation in usage code use Getopt::Long qw(:config auto_version auto_...= ($tSize < $qSize) ? 1 : 0; my $longTarget = (1 - $shortTarget);...* 4)]; my $lLen = $fields[10 + ($longT...2305 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2261 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!def...2151 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 328...
2206 days ago
