Results for "k-mer"
Blogs
Bioinformatics tools for telomere to telomere assembly !
● Merfin – k-mer-based assembly and variant calling evaluation for improved consensus acc...ence built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, s...984 days ago
Frequently used bioinformatics tools for viral genome analysis !
...: GAGE: A critical evaluation of genome assemblies and assembly algorithms. Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012). KMC: Disk-based k-mer counting on a PC. Deorowicz,...1039 days ago
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Bookmarks
- ...omprehensive, and integrates read quality, mate pair orientation and insert length (for paired-end reads), sequencing coverage, read alignment and k-mer frequency. ALE pinpoints synt...
2923 days ago
- ...lanation of the parameters. 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...
2697 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
...iant sequences in bacteria. VelvetK 20120606 – Find a reasonable K-mer size to Assemble Genome Reads with VelvetVelvetK can estimate the best k-mer size to use for your Velvet d...2677 days ago
Top-level pages
Commercial and public next-gen-seq (NGS) software
...find semiglobal non-gapped alignments based on k-mer seeds. http://bibiserv.techfa...find semiglobal non-gapped alignments based on k-mer seeds. Authors are Kim Rasmus...netics. SSAKE - The Short Sequence Assembly by K-mer search and 3' read Extension...3511 days ago
Software packages for next gen sequence analysis
...; a very fast program to find semiglobal non-gapped alignments based on k-mer seeds. Authors are Kim Rasmus...titute for Molecular Genetics. * SSAKE - The Short Sequence Assembly by K-mer search and 3' read Extension...3234 days ago
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Bio-Scripts
- # 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
2256 days ago
Estimate Genome Size with Jellyfish and R
...umber of treads to be used in the run. eg: 1,2,3,..etc. #-C -both-strands Count both strands #-m -mer-len=unit32 Length of the k-mer #-s -size=unit32...2238 days ago
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Comments
Comment on "Short-read assembly using Spades !"
...contigs using a text editor or a genome browser. SPAdes also provides several options for tuning the assembly parameters, such as adjusting the k-mer length or enabling error corr...413 days ago
Comment on "Sibelia: A comparative genomics tool"
...------------------ Algorithm of "Sibelia" depends on presence of solid k-mers within syntenic regions. If...s of computations. Each stage has two parameters, K and D. Let's call K-mer a substring of length K. At e...1277 days ago
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