Results for "Next Generation Sequence Analysis"
Bio-Scripts
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; us...} # Return the type of the sequence as a human readable string s...dues)'; } # Concatenate two sequences together and return the resu...lass) if ref($class); my ($sequence,$type) = @_; my $self =...2195 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2158 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the ref...2154 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB:...Output type description ###### # cds - translated sequence (starting with ATG and ending...with a stop codon included) # cdna - transcribed sequence...2152 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [o..."SEQUENCE" PROCESSING Read Splitting Sequence data may be used in raw form...empty files FORMATTING Sequence -C|--dumpcs Fo...
2140 days ago
Install Parrot Virtual Machine !
#Parrot is a virtual machine designed to efficiently compile and..................no. auto::coverage - Are coverage analysis...00F specify hex value to use as hash seed -X --dynext add path to dynamic extension sea...1551 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-lin...tome assembly using three kinds of metrics: 1. sequence based (if --assembly is given...ontigs.csv [ INFO] 2018-07-13 14:54:40 : Writing analysis results to assemblies.csv
2137 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() { chomp; $ids{$_} += 1;...2109 days ago
- ...------------------- Coverage Analysis:...e library complexity from the sequence of read pairs FilterLong...ools that perform metagenomic analysis, e.g. microbial community com...ith GATK BWA tools CreateSequenceDictionary (Picard)...
2089 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.p...ameter not provided\n"; { local $/=">"; while() { chomp; next unl...2079 days ago
