Comment on "Sibelia: A comparative genomics tool"
...ces file 2. Dot file with resulting de Bruijn graph All these files are descri...s down the computation. Resulting de Bruijn graph ------------------------- F...actually performed with the genome behind the graph model. Suppose that somewhe...1301 days ago
Comment on "KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies"
...the kmer “noise” is part of the final assembly? What do you think contamination would look like in the kmer plot? What can the kmer graph tell you about the ploidy of...1353 days ago
Comment on "Estimate Genome Size"
...ounts -C -s 10000000000 -U 500 -t 30 /dev/fd/0 # generate a histogram jellyfish histo fastq.counts_0 > fastq.counts_0.histo # generate a pdf graph of the histogram jellyplot.p...1914 days ago
Comment on "Run miniasm assembler on nanopore reads !"
...hits remain after cut[M::ma_hit_contained::149.341*1.00] 18263 sequences and 142921 hits remain after containment removal[M::main] ===> Step 4: graph cleaning <===[M::ma_sg_gen...2297 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
urbe@urbo214b[genome] graphmap align -h []GraphMap - A very accurate and sens...e Sikic and Niranjan NagarajanGraphMap is licensed under The MIT...s FASTQ or FASTA files. gfa - Graphical Fragment Assembly format....Algorithmic options: -k INT Graph construction kmer size. [6] -...2308 days ago
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Comment on "Structural variation: the hidden genomic treasure"
...are suite. A high-speed next-gen sequencing structural variation caller. GRIDSS calls variants based on alignment-guided positional de Bruijn graph break-end assembly, split rea...2719 days ago
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Comment on "Bioinformatics Algorithm Demonstrations and Tutorials"
Application of graph theory algorithm for rapid protein side-chain prediction http://www.ncbi.nlm.nih.gov/pubmed/129309993723 days ago