Results for "Genome"

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  • String graph based genome assembly software and tools !

    In graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string".  String graphs were first proposed by E. W. Myers in a 2005 publication. In recent Genome Research paper describing an...

    Tags: String, graph, genome, assembly, software, tools !

    2281 days ago

  • Converting a VCF into a FASTA given some reference !

    Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528) This script has been modified by others to convert InDels as well, e.g. this by David Eccles ./vcf2fq.pl -f <input.fasta> <all-site.vcf> ...

    Tags: Convert, VCF, FASTA, reference, genome, assembly, phase

    2069 days ago

  • CANU genome assembly parameters !

    Choose the appropriate parameters to run Canu and run it. The assembly will take about an hour. You can use two cores (parameter -maxThreads=2) and you would like to disable cluster option, since we compute on a single Amazon server set off the option to compute on cluster useGrid=false...

    Tags: CANU, genome, assembly, parameters, NGS, LongReads, OLC

    1898 days ago

  • List of tools frequently used while genome assembly

    List of tools frequently used while genome assembly: I have used the following assemblers Spades (v. 3.10.1) CANU (v. 1.6) Unicycler (v. v0.4.1) Miniasm (v. 0.2-r137-dirty) I have used the following mappers minimap2 (v. 2.0rc1-r232) minimap (v. 0.2...

    Tags: List, tools, frequently, genome, assembly

    1883 days ago

  • Software for genome assembly !

    List of bioinformatics tools/Software Website References for genome assembly: 1 Falcon https://github.com/PacificBiosciences/pb-assembly 2 Canu assembler http://canu.readthedocs.io/en/latest/index.html 3 Miniasm assembler https://github.com/lh3/miniasm 4 PBJelly scaffolding tool https://...

    Tags: List, bioinformatics, tools, Software, Website, References, genome, assembly

    1297 days ago

  • Ancient whole genome duplication (WGD) detection tools !

    There are two methods for ancient WGD detection, one is collinearity analysis, and the other is based on the Ks distribution map. Among them, Ks is defined as the average number of synonymous substitutions at each synonymous site, and there is also a Ka corresponding to it, which refers to the av...

    Tags: wgd, duplication, whole, genome, plan, tools, software, synteny, list

    1108 days ago

  • Illumina based assembly pipeline steps !

    Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment (Bowtie 2) Sort and index alignments (SAMtools) Primer sequence removal (iVar; amplicon data only) Duplicate read marking (p...

    Tags: assembly, pipeline, genome, illumina

    830 days ago

  • Tools to detect synteny blocks regions among multiple genomes

    The synteny block (which etymologically means “on the same ribbon”) is a collection of contiguous genes located on the same chromosome. These block regions have mostly been preserved by genome rearrangements, and so synteny blocks from two related species (e.g., humans and mice) will ...

    Tags: Synteny, Genome, GWAS, Conserve Synteny, Synteny Blocks, Comparative Genomes, Syntenic Regions

    2563 days ago

  • Dynamic chromosome breakpoints !!!

    Cell division involves the distribution of identical genetic material, DNA, to two daughters’ cells. During this process, duplicated deoxyribonucleic acid (DNA) goes through a condensation and decondensation process. This is followed by nuclear envelope dissolution, mitotic spindle assembly...

    Tags: Bioinformatics, Genome, Chromosome, Breaks, Breakpoints, EBRs, Recombination, Cross-over, Abnormalities, DNA

    3505 days ago

  • Structural variation: the hidden genomic treasure

    Genome re-sequencing projects have revealed substantial amounts of genetic variation between individuals extending beyond single nucleotide polymorphisms (SNPs) and short indels. Structural Variations (SVs) and Copy Number Variations (CNVs) are a major source of genomic variation. However, compar...

    Tags: Bioinformatics, Chromosome, Genome, NGS, Structure Variation, Deletions, Insertions, Duplications, Inversions, Translocations

    2655 days ago