BBTools for bioinformatician !
...---------------------------------------------------Reformat.sh Count k-mers/find unknown primers  ...-------------kcompress.shNewest member of BBTools. Identify constituent k-mers. http://seqanswers.com/f...2313 days ago
Useful Bioinformatics Analysis Tools !
...ok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE, 2015; 10...lski, T., Grabowski, Sz., Deorowicz, S., Indexing arbitrary-length k-mers in sequencing reads, PLO...905 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...2911 days ago
2747 days ago
Frequent words problem solution by Perl
...ed with perl http://rosalind.info/problems/1a/ #Find the most frequent k-mers in a string.#Given: A DNA string Text and an integer k.#Return: All most frequent k-mers in Text (in any order).use st...3294 days ago
Commercial and public next-gen-seq (NGS) software
...SSAKE) 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...3561 days ago
Software packages for next gen sequence analysis
...SSAKE) 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...3284 days ago
3588 days ago
Clump Finding Problem Solved with Perl
#Find patterns forming clumps in a string. #Given: A string Genome, and integers k, L, and t. #Return: All distinct k-mers forming (L, t)-clumps in Genome. use strict; use warni...2376 days ago
2306 days ago
Comment on "Sibelia: A comparative genomics tool"
...------------------ Algorithm of "Sibelia" depends on presence of solid k-mers within syntenic regions. If...At each stage "Sibelia" constructs so called de Bruijn graph, graph of K-mers that occur in the genome, an...1327 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...1940 days ago