Installing Porechop on Ubuntu !
...o/top_level.txt writing manifest file 'porechop.egg-info/SOURCES.txt' reading manifest file 'porechop.egg-info/SOURCES.txt' reading manifest templ...t scores: match, mismatch, gap open, gap extend (default: 3,-6,-5,-...2146 days ago
Install Python locally on shared Linux server !
....7.11 #Then I compiled the source following its guideline ./...on by running the command: source ~/.bashrc_profile #You mig...to update our PATH variable. Open ~/.bashrc_profile and add the #...ad the session by the command source ~/.bashrc_profile or logout a...2138 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() {...LE; local $/ = "\n>"; # read by FASTA record open F...2136 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -file => "$ARGV[0].parts.fasta",-format=>'fasta'); open(S...2103 days ago
Perl script to split fasta sequence / overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "2083 days ago
Installing pb-assembly on Linux !
...OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAP...o_asm [jnarayan@hmem00 ~]$ source activate denovo_asm (den...8_1 conda-forge openssl: 1.0.2p-h470a237_0...1 py27_0 openssl 1.0.2p...2075 days ago
2067 days ago
Setting up falconUnzip conda environments for genome assembly !
...180 KB conda-forge pyopenssl-18.0.0 |...34 KB conda-forge intel-openmp-2019.1 |...conda-forge intel-openmp: 2019.1-144...############## | 100% intel-openmp-2019.1 | 885 KB | #######...2030 days ago
Perl script to split fasta sequence and create overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "2012 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::SeqIO; my ($sequence_data_r...with parameters $chr_set!\n"; } sub touch { my ($fn, $seq) = @_; open F...1727 days ago