Installing Busco version 4.0.6
(base) jit@jit-HP-Pro-3335-MT: conda install -c bioconda -c conda-forge busco=4.0.6 Collecting package...77 KB conda-forge r-base-3.6.0 |...r36h6115d3f_1002 62 KB conda-forge sepp-4.3.10....4.1-r36h6115d3f_1 r-rcolorbrewer conda-forge/noarch::...1500 days ago
2122 days ago
2122 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta my $minlen = shift or die "Err...2113 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -file => "$ARG...tig sequence my $seq = $seqobj->seq; my $lenseq=length $s...ontig my @regions=(); my @bases=split //,$seq; push(@ba.... "_p$cont"; $pseqobj->display_id("$new_id");...2110 days ago
2107 days ago
Generates a genome coverage plot with R
library(CoverageView) ##draw a coverage plot for a test case BAM file #get a BAM test file treatBAMfile2103 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toym...2100 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, "2090 days ago
Perl script to reverse complement a DNA sequence !
#!/usr/bin/perl -w $DNA = 'ACGGGAGGACGGGAAAATTACTACGGCATTAGC'; print "Here is the...reverse complement DNA: WRONG:\n\n"; print "$revcom\n"; print "\nThat was a bad algorithm, and the reverse...2090 days ago