Results for "kmer"
Bio-Scripts
Clump Finding Problem Solved with Perl
...TGCGACATAATGTACGAATGTAATGTGCCTATGGC"; my $subStr="?"; my $clump=4; my $kmer=5; for (my $aa=0; $aa $max...e (keys %myHash){ print "$name " if $myHash{$name} == $clump; } kmerMatch ($string, $subStr, $kmer...2345 days ago
- ...MD: jellyfish histo -t 40 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf CMD...sh dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa CMD finished (16 seconds...: jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa * Running CMD: jellyfish...
2139 days ago
Perl subroutine to creating kmer !
sub k_mers { my ($sequence, $k) = @_; my $len = length($sequence); my @result = (); for (my $i = 0; $i1579 days ago
- sub kmers { my $seq = shift or return; my $len = length $seq; my @kmers; for (my $i = 0; ($i + $KMER_SIZE)
1569 days ago
Tadpole is 250x faster than SPADes assembler !
...nput file for reads to use as kmer data. in2= Second i...emented) dump= Write kmers and their counts. fastadump...Store and count each kmer together and its reverse-comp...(em1) Min ratio between kmer depths to call an error. err...988 days ago
Perl script to rename the fasta file !
#Script #1 #!/usr/bin/perl -w use strict; #USAGE #perl extractPattern.pl kmerfasta > uniref100_result_broad my %kHash; local $/ = '>'; my $infile2 = "$ARGV[0]"; # Kmer fasta open( FH2, '870 days ago
Extract all fasta sequences except ids !
...red_without_omi.fasta > omi_single_id_plus_all.fa #Extract unique kmer ./uniquekmer -f omi_single_id_plus_all.fa...and number the kmers perl storeKmer.pl omi_kmer19_formated.fa > omi_kmer19_formated_numbered.fa # c...840 days ago
- #!/bin/bash #Counting k-mers for different k echo "k,unique,distinct,total" for k in {1..15}; do kat hist -o phiX_$k.hist -m $k phiX.fasta >/dev/null 2>&1 egrep -v '^#' phiX_$k.hist|awk '{if ($1==1) u=$2; d+=$2; t+=$2*$1;}\ END{print "'$k',"u","d","t}' done
806 days ago
