Installing pb-assembly on Linux !
...-> python-msgpack - pb-assembly -> mummer4 -> perl 5.22.0* Close matches found; did you mean one of...uiver.py fc_unzip.py fc_ctg_link_analysis fc-match fc_rr_ct...2047 days ago
1618 days ago
1566 days ago
Onliner to split the multifasta to singlefasta files !
#Split the multifasta to singlefasta # Multi fasta #Single fasta awk '$0 ~ "^>" { match($1, /^>([^:]+)/, id); filename=id[1]} {print >> filename".fa"}' sequence.fasta1414 days ago
Bash script to handle Multifasta files
...ut.fasta #Add ‘>’ at the beginning of headers in a FASTA file $ awk '{if ($0 ~/_/) {printf ">";} print $0; }' input.fasta > output.fasta #Match FASTA headers in two differen...1370 days ago
List of string comparison algorithms !
String comparison: Levenshtein Distance Damerau-Levenshtein Distance Jaro Distance Jaro-Winkler Distance Match Rating Approach Comparison Hamming Distance More at https://jellyfish.readthedocs.io/en/latest/comparison.html995 days ago
Perl script for Smith-Waterman Algorithm
...die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2) = @ARGV; # scoring scheme my $MATCH = 1; # +1 for letters that match my $MISMATCH = -1; # -1 for...963 days ago
Raku script to find overlaps between two bed files !
...plit("\t"); my $chr2 = @fields2[0]; my $start2 = @fields2[1]; my $end2 = @fields2[2]; # Check for chromosome match and overlap if $chr1...107 days ago
Perl script to find overlaps between two bed files !
#!/usr/bin/perl use strict; use warnings; # Check if the correct number of arguments are provided if (@ARGV != 2) { die "Usage: $0 file1.bed file2.bed\n"; } # Read the contents of the two BED files my $file1 = shift @ARGV; my $file2 = shift @ARGV; open my $fh1, '107 days ago