Results for "Diploid"
Blogs
Computer simulation of genetic mechanism !!
...hey/software/software.htm#fpg FREGENE FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. http://www.ebi.a...2969 days ago
Software and Tools to detect structure variation with long reads !!
...llip;the first long-read characterization of structural variation in a diploid human personal genome…...uctural variation in a personal genome—towards a human reference diploid genome” More at h...2602 days ago
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Bookmarks
Assembly and diploid architecture of an individual human genome via single-molecule technologies
The research work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach refer...3215 days ago
- HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assem...
1087 days ago
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Top-level pages
List of generic simulation software/tools/resource with brief description and homepage !!!
...p://genfaculty.rutgers.edu/hey/software#fpgFREGENE FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. http://www.ebi.a...3731 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...mplemented in C and uses SAMtools API; latest version should work with diploid genomes Input: requires BAM...saac Variant Caller Description: detects SNPs and small indels from diploid sample; designed to run on &l...2903 days ago
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News
Phased Human Genome Assembly !
...The genome was then de novo scaffolded using Phase Genomics’ Proximo Hi-C platform, resulting in the first chromosome-scale diploid assembly of a single individu...2030 days ago
Video
TEDxCaltech - J. Craig Venter - Future Biology
...ig Venter is a biologist most known for his contributions, in 2001, of sequencing the first draft human genome and in 2007 for the first complete diploid human genome. In 2010 he and...3857 days ago
Bio-Scripts
- ...GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t a...GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t a...GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t a...
922 days ago
Bash script to simulate a genome !
...er.fasta.gz # Convert to diploid with approximately 2% heteroz...5.1_ASM340174v1_genomic.fna_upper.diploid.vcf.gz \ out=GCA_003401745.1...# get only 1 haplotype from the "diploid" reference bgzip -@75 -dc GC...5.1_ASM340174v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t a...912 days ago
Tags
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initi...Tags: dipSPAdes, Assembler, Highly, Polymorphic, Diploid, Genomes
2322 days ago
- HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliabl...
Tags: HaploMerger2, rebuild, haploid, sub-assemblies, high-heterozygosity, diploid, genome, assembly
2041 days ago
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Comments
Comment on "Calling variants in non-diploid systems"
FreeBayes is widely used for calling variants in diploid systems. However, it can also be used for calling variants in pooled samples where the number of samples is not known. This is...1038 days ago
