3214 days ago
BBTools for bioinformatician !
...king of low-complexity repetitive kmers, which is not usually a probl...------------Reformat.sh Count k-mers/find unknown primers  ...ly, the command means "look for 25-mers in the leftmost 25 bp of the...ch tells you the number of unique kmers in each peak on the histogram...2416 days ago
Useful Bioinformatics Analysis Tools !
...k, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE, 2015; 10...ski, T., Grabowski, Sz., Deorowicz, S., Indexing arbitrary-length k-mers in sequencing reads, PLO...1009 days ago
Kraken: ultrafast metagenomic sequence classification using exact alignments
...forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classificati...3014 days ago
2850 days ago
Frequent words problem solution by Perl
...nd.info/problems/1a/ #Find the most frequent k-mers in a string.#Given: A DNA str...t and an integer k.#Return: All most frequent k-mers in Text (in any order).use st...max;}sub kmerMatch { #Check the exact matching kmers with sliding windowmy ($strin...3398 days ago
Commercial and public next-gen-seq (NGS) software
...SAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Auth...3664 days ago
Software packages for next gen sequence analysis
...SAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Auth...3388 days ago
3692 days ago
Clump Finding Problem Solved with Perl
...ven: A string Genome, and integers k, L, and t. #Return: All distinct k-mers forming (L, t)-clumps in Geno...($string, $subStr, $kmer); sub kmerMatch { #Check the exact matching kmers with sliding window my ($str...2479 days ago
2410 days ago
Comment on "Sibelia: A comparative genomics tool"
...----------------- Algorithm of "Sibelia" depends on presence of solid k-mers within syntenic regions. If...t each stage "Sibelia" constructs so called de Bruijn graph, graph of K-mers that occur in the genome, an...1430 days ago
Comment on "Estimate Genome Size"
# count k-mers (see jellyfish documentation for options) gzip -dc reads1.fastq.gz reads2.fastq.gz | jellyfish count -m 31 -o fastq.counts -C -s 10000000000 -U 500 -t 30 /d...2043 days ago