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...989 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,...1044 days ago
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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...2683 days ago
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...3516 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...3240 days ago
2262 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...2243 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, whic...Tags: COPE, accurate, k-mer, pair-end, reads, connection, tool, genome, assembly
2340 days ago
Musket: a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in ...Tags: Musket, multistage, k-mer, spectrum, corrector
2340 days ago
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...418 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...1282 days ago