Results for "k-mers"
Blogs
BBTools for bioinformatician !
...---------------------------------------------------Reformat.sh Count k-mers/find unknown primers ...-------------kcompress.shNewest member of BBTools. Identify constituent k-mers. http://seqanswers.com/f...2283 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...876 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...2881 days ago
- ...eters. 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...
2718 days ago
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Pages
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...3265 days ago
Top-level pages
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...3531 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...3255 days ago
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Wire posts
News
- ...ads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn grap...it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats...
3559 days ago
Bio-Scripts
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...2346 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
2277 days ago
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merqury: Evaluate genome assemblies with k-mers
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this ...Tags: merqury, Evaluate, genome, assemblies, k-mers
1414 days ago
Metabuli 분리 improves metagenomic read classification
Metabuli 분리 improves metagenomic read classification through metamers, DNA-AA k-mers, to be sensitive and specific, recovering 99% and 98% of DNA or AA classifiers. Metabuli is metagenomic classifier that jointly analyze both DNA and amino acid (AA) sequences. DNA-based classifiers can m...Tags: Metabuli, 분리, metagenomic, read, classification, metamers, DNA-AA, k-mers, sensitive, and specific, DNA, AA, classifiers
349 days ago
Comments
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...1297 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...1910 days ago
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