Results for "Mers"
Users
About me: ...n the field of Bioinformatics,Genomics,Genetics,Cheminformatics and Life Science. I recruit talanted individuals from Bioinformatics to Sas Programmers to Research Scientists. I co...3096 days ago
Blogs
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...2298 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...891 days ago
Bookmarks
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...2896 days ago
- ...ters. For more information, refer to the manual. KmerGenie can be used to determine the best k-mer size, minimum abundance of correct k-mers, and genome size estimation f...
2733 days ago
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Pages
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 ($strin...3280 days ago
Top-level pages
Commercial and public next-gen-seq (NGS) software
...SAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Auth...3546 days ago
Software packages for next gen sequence analysis
...SAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Auth...3270 days ago
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Wire posts
News
- ...ds that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn grap...t detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats...
3574 days ago
Bio-Scripts
Clump Finding Problem Solved with Perl
...ven: A string Genome, and integers k, L, and t. #Return: All distinct k-mers forming (L, t)-clumps in Geno...($string, $subStr, $kmer); sub kmerMatch { #Check the exact matching kmers with sliding window my ($str...2361 days ago
- # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19
2292 days ago
- +3 more Bio-Scripts
Tags
UniqueKmer: Generate unique KMERs for every contig in a FASTA file
Generate unique k-mers for every contig in a FASTA file. Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands). This tool accepts the input of a FASTA file consisting of ...Tags: Unique, Kmer, Mers, Contigs, FASTA, Genome
898 days ago
Comments
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...1312 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...1925 days ago
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